[R] Nonlinear programming problem
Hello useRs, I'm using the command solnp in package Rsolnp to solve a general nonlinear programming problem. But I got an error that the leading minor of order 15 is not positive definite . Can anybody tell what may cause this error? Does it have something to do with the starting values? Thanks a lot!!! Xiaoxi [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Calculate difference between dates in years
Just expanding on Brians code to something that will work for vector.
age_years - function(first, second)
{
lt - data.frame(first, second)
age - as.numeric(format(lt[,2],format=%Y)) -
as.numeric(format(lt[,1],format=%Y))
first
as.Date(paste(format(lt[,1],format=%Y),-,format(lt[,2],format=%m-%d),sep=))
age[which(first
as.Date(paste(format(lt[,1],format=%Y),-,format(lt[,2],format=%m-%d),sep=)))]
- age[which(first
as.Date(paste(format(lt[,1],format=%Y),-,format(lt[,2],format=%m-%d),sep=)))]
- 1
age
}
--
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Re: [R] Odp: Programming: loop versus vector oriented
Hi Jan but I think this is how your code really works. Did you try it? Regards Petr Jan private jrheinlaen...@gmx.de napsal dne 16.09.2010 13:22:05: Hello Petr, If you want to get results of your function for a vector of reynolds and dk you can use function outer and probably get rid of for cycle in the function. outer(c(100, 530,2410), c(10, 150,200),lambda_wall) [,1] [,2] [,3] [1,] 0.640 0.6400 0.6400 [2,] 0.1207547 0.12075472 0.12075472 [3,] 0.1081338 0.04515774 0.04515774 that gives me an array as an answer (and does more calculations than necessary, in this case 9 instead of 3). The result should be a vector. The function should work on the nth elements of the two input vectors and put the result into the nth element of the output vector. So it would work like c - a + b, only instead of '+' there are more complex calculations. Best regards, Jan __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Question: how to obtain the clusters of genes (basically the ones in the row dendrograms) from an object obtained by heatmap.2 function
Hello Sunny, Defining groups at a given height can be done with the cut function (see ?cut.dendrogram). Unfortunately, cut doesn't give you the option of specifying a number of clusters rather than a height in the way that cutree does for hclust objects. Perhaps someone else here knows of a package that includes a function to do this (I did a quick sos search but didn't find anything obvious). Otherwise you could examine the cut function and try to hack a version that takes number of groups as an argument. You can see the function's code with the command getS3method(cut, dendrogram). Sorry I can't help more. Being a simple soul I find hclust objects so much easier to deal with ! Michael On 17 September 2010 11:30, Sunny Srivastava research.b...@gmail.com wrote: Hello R-Helpers, I have a question about extracting the clusters of genes after we make the heatmap (say ht4) using the heatmap.2 function. Basically, I want to get the clusters which are shown as row dendrogram in the heatmap. I understand that ht4$rowDendrogram is an object of dendrogram and it containes details of all the nodes and branches, but lets say I want to know the number of clusters and the genes in each cluster if I terminated the tree (dendrogram) at a particular height. Also, if I know that I want 12 clusters, how do I know which height I should terminate the tree (or branching structure) I am sorry if I am not clear. Please let me know if you need any further clarifications. Thanks in advance for your help. Best Regards, S. PS: I had posted this question on the Bioconductor mailing list, but no one responded with the answer about my problem (some suggested to use other package). Probably this is more related to R, so I am reposting here. Below is the dump of the matrix *row.scaled.fc2* and the object *ht4* which was obtained by using the heatmap.2 function. - Dump of the matrix row.scaled.fc2 of dimension 47X4 for which I need to get the cluster - row.scaled.fc2 - structure(c(1.28370586906697, 0.045882176168387, -1.36708804887146, 0.521861081643557, 0.931917365795697, -1.26811754842825, -0.72130612803134, 0.997233560332114, 1.10914280037357, 0.906822512746599, 0.124305385892705, 0.243716750638903, -0.81506628597585, 0.9281945227055, -1.02514155647985, -0.0148828263869010, 0.610771143828774, -1.31512789127346, -1.03419747081316, -1.37364737258546, 1.25426184614502, -0.901983912371582, 1.39208493297302, 1.46330419386939, 1.46904838309704, 1.33893188130515, 1.19407808189758, 1.2218547353343, 1.19698274357976, 1.18155526998177, 0.841732283108634, 0.747807260442244, 0.714318042078153, -1.33532716080095, -0.313607205847584, 0.355541486307312, -0.116351310506438, 0.77912190137299, 1.19372966187956, -1.46614749631243, 1.05871763558761, -0.943184299406566, 1.03714731356991, 1.25047276064487, 0.851530489918317, 0.97326112450597, 0.776853817614179, 0.254354524536168, 1.31978778177031, 1.03174081073449, 1.03284070831524, 0.653353551741362, -0.215733545477378, -0.966047927590969, 0.652368565446036, 0.536560120952493, 0.807139899513123, 1.26763097889282, 1.28335333872251, 1.45704025225707, 0.57691754078049, 1.07113369815538, 0.610158458070122, -0.762088920575592, 1.00819322156949, 1.14148232415467, 0.297815716619546, 0.143195107796418, -0.0065855621849476, 0.062650188298147, -0.177601977084224, -0.437288024655434, 0.178377570495840, 0.447251122498145, 0.400521563178456, 0.441487949431983, 0.46509369129, 0.754248218272813, 0.657576754588525, 0.832332574891687, -0.194585070239614, 1.09572866565514, 1.04256940502540, 0.583290457043162, 0.947182223637108, 0.453501818870319, 0.362539212141846, 0.64658837487362, 0.778492522245523, 0.406650195058153, -0.113538768459753, 0.596257630693658, 0.652082611403661, 0.731202922578465, -0.540351240198989, -0.280636135117373, 0.0957282195118376, -0.301771114678491, -0.319287162711085, 0.392333008215492, 0.595799016736027, -0.493631246722725, -0.570129842719142, -0.687622802632555, -0.243797611378268, -0.510913960310597, -0.263387651214153, -0.172495725682589, 0.609736001727743, 0.809229072877685, 1.08430415610192, 0.475088705288397, 0.503896215545131, 0.0658502505817462, -0.235112572720005,
Re: [R] KMedians clustering in R
Thanks all. But I was looking for KMedian algorithm and not the KMedoids
algorithm. The wiki says, Note that this algorithm is often confused with
k-medoids, which finds the optimal medoid, not median, for each cluster. (A
medoid is an actual point from the dataset; a median is the mathematical median
calculated separately for each dimension.)
Any package which does KMedian clustering algorthm? Many Thanks.
Regards,
Shubha.
-Original Message-
From: Christian Hennig [mailto:chr...@stats.ucl.ac.uk]
Sent: Thursday, September 16, 2010 9:32 PM
To: Shubha Vishwanath Karanth
Cc: r-help@r-project.org; r-h...@stat.math.ethz.ch
Subject: Re: [R] KMedians clustering in R
pam/clara in package cluster are probably as close to it as you can be.
There is no unique definition of a multivariate median and therefore there
is no unique definition of k-medians, but pam/clara is one possible
version of it. (Of course if you think of k-medians as defined in a
specific paper, it may still be something slightly different.)
Christian
On Thu, 16 Sep 2010, Shubha Vishwanath Karanth wrote:
Hi R,
Is there a package in R to perform KMedian clustering?
Thanks.
Shubha
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*** --- ***
Christian Hennig
University College London, Department of Statistical Science
Gower St., London WC1E 6BT, phone +44 207 679 1698
chr...@stats.ucl.ac.uk, www.homepages.ucl.ac.uk/~ucakche
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Re: [R] R Founding
On 09/17/2010 12:14 AM, Jeremy Miles wrote: I know from organizing a conference in Germany that the only really good way was and is ordinary money transfer via BIC and IBAN numbers. Unfortunately, this system is pretty unknown in the US. Europeans can easily use money transfer to the R foundation. Paypal? Many open source projects have a 'donate with paypal' button. Jeremy As far as I remember, this requires that a real person opens the account, and takes on the associated tax issues. It may be different for US-based projects. Another option is to get the hosting institutions to accept credit cards, but they tend to balk at the transaction costs (with the result that conference organizers get driven to conference agencies with much greater handling fees...) But seriously, even Springer can do wire transfers nowadays. Maybe we should just wait for the US banks to join the 21st century? -- Peter Dalgaard Center for Statistics, Copenhagen Business School Phone: (+45)38153501 Email: pd@cbs.dk Priv: pda...@gmail.com __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Converting tables to matrices
Thanks so much! I realise that probably seems very simple to you, but you've just saved me hours of struggling with syntax and commands I'm not very familiar with...excellent. Cheers, Selthy -- View this message in context: http://r.789695.n4.nabble.com/Converting-tables-to-matrices-tp2543309p2543423.html Sent from the R help mailing list archive at Nabble.com. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Question: how to obtain the clusters of genes (basically the ones in the row dendrograms) from an object obtained by heatmap.2 function
Thanks Michael for your help. At least its good to know that there is no function which does what I wanted. I will definitely try to code something that fulfills my requirements. Regards, S. On Fri, Sep 17, 2010 at 2:32 AM, Michael Bedward michael.bedw...@gmail.comwrote: Hello Sunny, Defining groups at a given height can be done with the cut function (see ?cut.dendrogram). Unfortunately, cut doesn't give you the option of specifying a number of clusters rather than a height in the way that cutree does for hclust objects. Perhaps someone else here knows of a package that includes a function to do this (I did a quick sos search but didn't find anything obvious). Otherwise you could examine the cut function and try to hack a version that takes number of groups as an argument. You can see the function's code with the command getS3method(cut, dendrogram). Sorry I can't help more. Being a simple soul I find hclust objects so much easier to deal with ! Michael On 17 September 2010 11:30, Sunny Srivastava research.b...@gmail.com wrote: Hello R-Helpers, I have a question about extracting the clusters of genes after we make the heatmap (say ht4) using the heatmap.2 function. Basically, I want to get the clusters which are shown as row dendrogram in the heatmap. I understand that ht4$rowDendrogram is an object of dendrogram and it containes details of all the nodes and branches, but lets say I want to know the number of clusters and the genes in each cluster if I terminated the tree (dendrogram) at a particular height. Also, if I know that I want 12 clusters, how do I know which height I should terminate the tree (or branching structure) I am sorry if I am not clear. Please let me know if you need any further clarifications. Thanks in advance for your help. Best Regards, S. PS: I had posted this question on the Bioconductor mailing list, but no one responded with the answer about my problem (some suggested to use other package). Probably this is more related to R, so I am reposting here. Below is the dump of the matrix *row.scaled.fc2* and the object *ht4* which was obtained by using the heatmap.2 function. - Dump of the matrix row.scaled.fc2 of dimension 47X4 for which I need to get the cluster - row.scaled.fc2 - structure(c(1.28370586906697, 0.045882176168387, -1.36708804887146, 0.521861081643557, 0.931917365795697, -1.26811754842825, -0.72130612803134, 0.997233560332114, 1.10914280037357, 0.906822512746599, 0.124305385892705, 0.243716750638903, -0.81506628597585, 0.9281945227055, -1.02514155647985, -0.0148828263869010, 0.610771143828774, -1.31512789127346, -1.03419747081316, -1.37364737258546, 1.25426184614502, -0.901983912371582, 1.39208493297302, 1.46330419386939, 1.46904838309704, 1.33893188130515, 1.19407808189758, 1.2218547353343, 1.19698274357976, 1.18155526998177, 0.841732283108634, 0.747807260442244, 0.714318042078153, -1.33532716080095, -0.313607205847584, 0.355541486307312, -0.116351310506438, 0.77912190137299, 1.19372966187956, -1.46614749631243, 1.05871763558761, -0.943184299406566, 1.03714731356991, 1.25047276064487, 0.851530489918317, 0.97326112450597, 0.776853817614179, 0.254354524536168, 1.31978778177031, 1.03174081073449, 1.03284070831524, 0.653353551741362, -0.215733545477378, -0.966047927590969, 0.652368565446036, 0.536560120952493, 0.807139899513123, 1.26763097889282, 1.28335333872251, 1.45704025225707, 0.57691754078049, 1.07113369815538, 0.610158458070122, -0.762088920575592, 1.00819322156949, 1.14148232415467, 0.297815716619546, 0.143195107796418, -0.0065855621849476, 0.062650188298147, -0.177601977084224, -0.437288024655434, 0.178377570495840, 0.447251122498145, 0.400521563178456, 0.441487949431983, 0.46509369129, 0.754248218272813, 0.657576754588525, 0.832332574891687, -0.194585070239614, 1.09572866565514, 1.04256940502540, 0.583290457043162, 0.947182223637108, 0.453501818870319, 0.362539212141846, 0.64658837487362, 0.778492522245523, 0.406650195058153, -0.113538768459753, 0.596257630693658, 0.652082611403661, 0.731202922578465, -0.540351240198989, -0.280636135117373, 0.0957282195118376, -0.301771114678491, -0.319287162711085,
Re: [R] Question: how to obtain the clusters of genes (basically the ones in the row dendrograms) from an object obtained by heatmap.2 function
Cool. If you get some code working and don't mind sharing it please post it here. Michael On 17 September 2010 16:49, Sunny Srivastava research.b...@gmail.com wrote: Thanks Michael for your help. At least its good to know that there is no function which does what I wanted. I will definitely try to code something that fulfills my requirements. Regards, S. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] Simple question, name of the variable as string.
Dear R users, I have a very simple question and I've tried to search for the answer. (But failed.) there should be a function (func) that work like abc - c(1,2,3,4) func(abc) abc I would like to know the name of that function. Thank you very much for your help. Regards, CH -- CH Chan __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Simple question, name of the variable as string.
On Sep 17, 2010, at 2:54 AM, C.H. wrote: Dear R users, I have a very simple question and I've tried to search for the answer. (But failed.) there should be a function (func) that work like abc - c(1,2,3,4) func(abc) abc func - function(xyz) deparse(substitute(xyz)) func(abc) [1] abc I would like to know the name of that function. -- David. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] R Founding
-BEGIN PGP SIGNED MESSAGE- Hash: SHA1 On 17/09/10 08:38, Peter Dalgaard wrote: On 09/17/2010 12:14 AM, Jeremy Miles wrote: I know from organizing a conference in Germany that the only really good way was and is ordinary money transfer via BIC and IBAN numbers. Unfortunately, this system is pretty unknown in the US. Europeans can easily use money transfer to the R foundation. Paypal? Many open source projects have a 'donate with paypal' button. Jeremy As far as I remember, this requires that a real person opens the account, and takes on the associated tax issues. It may be different for US-based projects. Another option is to get the hosting institutions to accept credit cards, but they tend to balk at the transaction costs (with the result that conference organizers get driven to conference agencies with much greater handling fees...) But seriously, even Springer can do wire transfers nowadays. Maybe we should just wait for the US banks to join the 21st century? 1) I agree Jaroslaw - you can not buy the motivation you get from participants who are doing it for the love of it, but especially now, in tweaking out issues like memory usage and multicore, which effectively are issues with which the user is only indirectly confronted (Wow - in this release I can load a data.frame of 3GB... That's brilliant) would be very suitable to be done by paid developers who have long working expertise in these fields. I agree that the further development on the outside (cli, packages, ...) will be most effectively done as it is now - - by enthusiasts --- It worked so far, and why change it? Especially as the main problems seem to be with the internal internals. 2) I just looked at GRASS and qgis - both have donate buttons ( see http://grass.fbk.eu/donation.php and http://www.qgis.org/en/sponsorship.html ). Foundations to GRASS are managed through the Italien OSGeo Chapter. Maybe something similar would be an option for R as well? 3) Funding not only has to contribute to financing coding, but also to organise conferences, support participants, organise courses, etc. Cheers, Rainer - -- Rainer M. Krug, PhD (Conservation Ecology, SUN), MSc (Conservation Biology, UCT), Dipl. Phys. (Germany) Centre of Excellence for Invasion Biology Natural Sciences Building Office Suite 2039 Stellenbosch University Main Campus, Merriman Avenue Stellenbosch South Africa Tel:+33 - (0)9 53 10 27 44 Cell: +27 - (0)8 39 47 90 42 Fax (SA): +27 - (0)8 65 16 27 82 Fax (D) : +49 - (0)3 21 21 25 22 44 Fax (FR): +33 - (0)9 58 10 27 44 email: rai...@krugs.de Skype: RMkrug -BEGIN PGP SIGNATURE- Version: GnuPG v1.4.10 (GNU/Linux) Comment: Using GnuPG with Mozilla - http://enigmail.mozdev.org/ iEYEARECAAYFAkyTE8MACgkQoYgNqgF2egquPQCbBGUve3/cLj6focACw7OFHrBx uPkAnjM2r2r1crizQJKKMxKInMQM5/2Y =dlem -END PGP SIGNATURE- __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Simple question, name of the variable as string.
On Fri, Sep 17, 2010 at 7:54 AM, C.H. chainsawti...@gmail.com wrote: Dear R users, I have a very simple question and I've tried to search for the answer. (But failed.) there should be a function (func) that work like abc - c(1,2,3,4) func(abc) abc I would like to know the name of that function. Thank you very much for your help. Think: where does R do this? Answer: zzz = 1:10 ; plot(zzz) # look at the y axis. How did it do this? Look at the code. Type 'plot' without () and there's the code. Somewhere in there you will see where it sets the Y axis label, or ylab. Then read and understand the help pages for those functions. What happens if I do func(c(1,2,3,4))? What's the name of 'c(1,2,3,4)'? Its a good way to learn. Barry __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] R Founding
On Fri, 17 Sep 2010, Peter Dalgaard wrote: On 09/17/2010 12:14 AM, Jeremy Miles wrote: As far as I remember, this requires that a real person opens the account, and takes on the associated tax issues. It may be different for US-based projects. Nope -- all around the world, the governments think they should have an ability to look into who is receiving a money flow, and as banks and central banks operate within nation states, I suppose they can enforce that ;) But seriously, even Springer can do wire transfers nowadays. Maybe we should just wait for the US banks to join the 21st century? In the US the process is called an 'ACH' -- automated clearing house -- transfer, and if one has a destination payee name, destination bank name and routing number, and destination bank account number or account number with that destination payee, it is the mattter of a few second's work with a 'online bill payment' interface to make such transfers The trick is that the variance and differing models of national rules about what is permissible, and optionally, tax deductable as a charitable contribution, vary all around the world, and everyone wants to transfer to something and in a way they understand donation gridlock results until a donor someone simply asks (as has need done here) and the recipient someone engages to get the details solved. I've worked through these details in some detail with CentOS and if the principals of the R foundation want more information, please contact me offlist [some of the questions as to organizational specifics are in a space where some personal data privacy matters come into play, and need not be aired on a public and archived mailing list] -- Russ herrold __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] Markov Model problem
First, I don't have the correct lingo for this topic, so I can't really find a solution for my problem. And maybe I formulate it incorrectly, so bear with me. How would I calculate a 'constant transition matrix' if I know a given value at a given time? Let's say I know that my value is 54,0 at t=12. How do I get the initial chain value? t markov.growth 00 00.0 01 06.3 - My value of interest... 02 12.1 03 17.7 04 22.8 05 27.7 06 32.2 07 36.4 08 40.4 09 44.2 10 47.7 11 50.9 12 54.0 - These two is what I know... 13 56.9 14 59.6 15 62.1 I can't find out how to do this kind of 'reversed' calulation. Maybe there is some library that can do this for me? I know that there are a lot of packages covering different aspects of Markov Models. But my ignorance prevents me from finding out which one. TIA __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Help with customizing a histogram figure
On 09/16/2010 11:40 PM, Josh B wrote: Hi all, Please consider the following code: require(plotrix) l- list(rnorm(50),rnorm(50,sd=2),rnorm(50,mean=3)) multhist(l) I have two things I need help with: (1) In the output, there are empty spaces on the x-axis. How would I eliminate these spaces? I want a nice, smooth, empty-spaceless x-axis. (2) How could I add tracing lines to each histogram? I am undoubtedly using the wrong terminology. What I want to do is something like this: http://addictedtor.free.fr/graphiques/RGraphGallery.php?graph=55 Note that each histogram has a tracing line that summarizes the histogram. In summary, I'd like to modify the code above to (1) get rid of the dead spaces on the x-axis, and (2) add lines that traces to each of the histograms therein (all on the same graph). I am very bad at using R graphics at this point, so I need some pretty serious hand-holding. Exact code that gets the job done would be most useful for me. Thanks very much in advance! Hi Josh, You can get rid of the spaces like this: multhist(l,space=c(0,0)) By tracing lines I think you mean smoothed densities of your three samples. The addictedtor site seems to be down at the moment, so I can't check the page suggested by Thomas and Jorge. This is a bit more complicated, as the functions underlying multhist don't usually place the bars at values corresponding to the intervals you need to calculate. Perhaps if you use multhist to calculate the histograms: lhist-multhist(l,plot.it=FALSE) Then plot the histogram with barp instead (barp places bars on integer values by default and this happens to match your breakpoints): barp(lhist$out,names.arg=seq(-5.5,4.5,by=1), col=c(gray20,gray50,gray80))) calculate the density: l1dens-density(l[[1]]) and then display the lines: # notice the x offset and the rescaling of the density values lines(l1dens$x+6.5,rescale(l1dens$y,c(0,20))) repeating for the other two samples, you can get the plot you want. Jim __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Markov Model problem
On 17-Sep-10 08:19:20, Stefan Petersson wrote: First, I don't have the correct lingo for this topic, so I can't really find a solution for my problem. And maybe I formulate it incorrectly, so bear with me. How would I calculate a 'constant transition matrix' if I know a given value at a given time? Let's say I know that my value is 54,0 at t=12. How do I get the initial chain value? t markov.growth 0000.0 0106.3 - My value of interest... 0212.1 0317.7 0422.8 0527.7 0632.2 0736.4 0840.4 0944.2 1047.7 1150.9 1254.0 - These two is what I know... 1356.9 1459.6 1562.1 I can't find out how to do this kind of 'reversed' calulation. Maybe there is some library that can do this for me? I know that there are a lot of packages covering different aspects of Markov Models. But my ignorance prevents me from finding out which one. TIA Am I correct to assume that the information you intend to work from is that (here Y denotes the markov.growth variable): At t = 00, Y = 00.0 (initial state) At t = 12, Y = 54.0 ?? From this information alone, it is impossible to calculate any transition matrix for the evolution of the process, without making some assumption about a generic law of growth. However, taking the values you have supplied, I can see that: Y - c(00.0,06.3,12.1,17.7,22.8,27.7,32.2,36.4,40.4, 44.2,47.7,50.9,54.0,56.9,59.6,62.1) t.diff-(0:14) plot(t.diff,log(diff(Y))) looks like a very close approximation to a straight line, with a little random variation. So: Z - log(diff(Y)) LM - lm(Z ~ t.diff) LM$coeff # (Intercept) t.diff # 1.8369463 -0.0650716 And then: lines(t.diff, 1.8369463 - 0.0650716*t.diff) shows that the fit is very close, and it looks as though the random deviations have the same degree of dispersion over time (though there may be some evidence of serial correlation in these). Hence one could adopt a model log(Y[t+1] - Y[t]) = a + b*t.diff + error where a = 1.8369463, b = -0.0650716, or Y[t+1] = Y[t] + A + B^t where A = exp(a), B = exp(b). Then, since Y[0] = 0, for t=1,2,... Y[t] = t*A + B + B^2 + ... B^t Now, assuming a model *of this form* -- i.e. without knowing the values of A and B, you could use the (assumed above) information that Y[0] = 0, Y[12] = 54.0, to solve this for values of A and B. Then you could evaluate this for your value of interest Y[1]. However, incorporation of uncertainties due to the random error between observed values and the fit would be more complicated (and cannot be done given only the information about Y[0] and Y[12]). Note that this approach, given only Y[0] and Y[12], depends on *assuming* a model of the form Y[t+1] = Y[t] + A + B^t, whereas I was led to suggest this as an approach on the basis of looking at *all* the values you supplied. Just thoughts! Probably others can suggest ways of taking this further, or approaching it differently. Ted. E-Mail: (Ted Harding) ted.hard...@manchester.ac.uk Fax-to-email: +44 (0)870 094 0861 Date: 17-Sep-10 Time: 10:30:41 -- XFMail -- __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] R Founding
Hi, I would GLADLY donate 30-50$ each year just to see R develop, but there needs to be a way for me to do it in a civilized manner. If the userbase of R is over 2 million there will surely be 100,000 users who, like myself, will happily fork out 40$ a year - would that help? you can do the calculation yourselves. Set up a donation page in which I will be able to pay by credit card or PayPal and you will start getting donations from individual users. Advertise this at the startup message of the program: say something like support us at www.suppoRtR.com and the money will start coming. I think this is a great idea! (I emailed to the address on the R page to that effect two days ago :) ) From the other replies, it seems there are three broad groups of obstacles: (1) Figure out the way to do it -- PayPal would be best for international users, but there are now alternatives to PayPal such as Moneybookers, who might do the same thing for those who want to pay and might be better for the recipient -- I don't know. (2) What the money is used for (3) Convince the people who can make the decision, i.e. the executives of the R foundation. I think (2) is a fake problem. I for one would not care if the money I donate is used for something I never use, or is even used inefficiently. I gain so much from R from other people's work, I would see my donation as a gift to them, and they could do with that gift what they want to. They could go have lots of beer, for all I care (unless it gets in the way of writing R, of course :) ) But one way around (3) might be even to have package developers accept donations for packages. Is there a way to take this off the r-help list to try to tackle this as a project? Maybe set up a small Google Group? Marianne BTW after reading in this thread about the donation form and the possbility to do IBAN, I went back to r-project.org and then found the link how to donate. I had not seen this when I looked a few days ago. You can say I'm stupid and didn't look hard enough, but from a usability/ marketing perspective this means even this cumbersome possibility is not salient enough at the moment. -- Marianne Promberger PhD, King's College London http://promberger.info R version 2.11.1 (2010-05-31) Ubuntu 9.04 __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Interpolate? a line
I would like to thank you again for your help. But it seems that the floor function (ceiling, round too) create more dots in the matrix that line really touches. unique( floor( cbind( seq(2,62, by=0.1), linefn(seq(2,62, by=0.1)) ) ) ) You can see that in the picture below http://yfrog.com/5blineswj So, how to select the only the cells that the line touches? I would like to thank you in advance for your help best Regards Alex From: David Winsemius dwinsem...@comcast.net Cc: Rhelp list r-help@r-project.org Sent: Wed, September 15, 2010 1:55:10 PM Subject: Re: [R] Interpolate? a line On Sep 15, 2010, at 7:24 AM, David Winsemius wrote: Replacing context: Hello everyone. I have created a 100*100 matrix in R. Let's now say that I have a line that starts from (2,3) point and ends to the (62,34) point. In other words this line starts at cell (2,3) and ends at cell (62,34). Is it possible to get by some R function all the matrix's cells that this line transverses? I would like to thank you for your feedback. Best Regards Alex On Sep 15, 2010, at 6:52 AM, Michael Bedward wrote: Hello Alex, Here is one way to do it. It works but it's not pretty :) If you want an alternative, consider that produces the Y cell indices (since the x cell indices are already 2:62): linefn - function(x) 3+((34-3)/(62-2)) *(x-2) findInterval(linefn(2:62), 3:34) [1] 1 1 2 2 3 3 4 4 5 5 6 6 7 7 8 8 9 9 10 10 11 11 12 12 13 13 14 [28] 14 15 15 16 17 17 18 18 19 19 20 20 21 21 22 22 23 23 24 24 25 25 26 26 27 27 28 [55] 28 29 29 30 30 31 32 # that seems off by two linefn(62) [1] 34 linefn(2) [1] 3 # but that checks out and I realized those were just indices for the 3:34 findInterval vector (3:34)[findInterval(linefn(2:62), 3:34)] [1] 3 3 4 4 5 5 6 6 7 7 8 8 9 9 10 10 11 11 12 12 13 13 14 14 15 15 16 [28] 16 17 17 18 19 19 20 20 21 21 22 22 23 23 24 24 25 25 26 26 27 27 28 28 29 29 30 [55] 30 31 31 32 32 33 34 ( no rounding and I think the logic is clearer.) But I also realized it didn't enumerate all the the cells were crossed either, only indicating which cell was associated with an integer value of x. Also would have even more serious problems if the slope were greater than unity. To enumerate the cell indices that were crossed, try: unique( floor( cbind( seq(2,62, by=0.1), linefn(seq(2,62, by=0.1)) ) ) ) [,1] [,2] [1,]23 [2,]33 [3,]44 [4,]54 [5,]55 [6,]65 [7,]75 [8,]76 snipping interior results [83,] 58 32 [84,] 59 32 [85,] 60 32 [86,] 60 33 [87,] 61 33 [88,] 62 34 That could probably be passed to rect() to illustrate (and check logic): rect(cellidxs[,1], cellidxs[,2], cellidxs[,1]+1, cellidxs[,2]+1, col=red) #redraw line : lines(2:62, 3+(34-3)/(62-2)*(0:60)) --David. interp - approx(c(2, 62), c(3, 34), method=linear, xout=2:62) m - matrix(c(interp$x, round(interp$y)), ncol=2) tie - m[,2] == c(-Inf, m[-nrow(m),2]) m - m[ !tie, ] You might want to examine the result like this... plot(m) # plots points lines(c(2,26), c(3, 34)) # overlay line for comparison you can add a grid with abline(v=2:62, h=3:34) Michael __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. David Winsemius, MD West Hartford, CT __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. David Winsemius, MD West Hartford, CT [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] using variable from for loop in naming new variables
Hi Jim,
First, I think it's better if you reply to the list, other users might
be interested and have better answers.
Second, as other replies showed you, using a list is actually way easier
than creating new objects every time. Check especially the reply from
Joshua Wiley, which gives you great examples and guidance.
Last, regarding rm(list=ls()), what's the point of creating new objects
in your loop if you remove them right after?! Maybe you intend to do
stuff on them first. Anyway, I don't use Emacs so not sure why you do it
that way. Just my limited opinion.
HTH,
Ivan
Le 9/17/2010 12:35, Maas James Dr (MED) a écrit :
Hi Ivan,
Thanks for suggestions, was just hoping to do it all in one step,
creating a list and then filling it all seems rather complicated ...
will look up *apply.
As for removing objects, I run R interactively from within Emacs (ESS)
and stuff hangs around for successive evaluations, not sure where it
came from so I clean it out every time ... is there a better way?
Thanks
Jim
Message: 65
Date: Thu, 16 Sep 2010 18:03:29 +0200
From: Ivan Calandra ivan.calan...@uni-hamburg.de
To: r-help@r-project.org
Subject: Re: [R] using variable from for loop in naming new variables
Message-ID: 4c923fd1.8000...@uni-hamburg.de
Content-Type: text/plain
Hi!
assign() should do the job.
But using a list, and filling each element iteratively (with a for loop
or with *apply() ) might be better, up to you.
Btw, why do you remove your objects?
HTH,
Ivan
Le 9/16/2010 17:44, Maas James Dr (MED) a ?crit :
Simple one here ... but can't get it to work ...
for (i in 1:4){
paste(stuff,[i]),sep=)- 3 + i
}
ls()
rm(list=ls())
I just want it to create 4 new variables called stuff1, stuff2,
stuff3, stuff4 with the corresponding assignments. I realise that
there are more elegant functions but this is just a model of a bigger
situation.
Thanks
Jim
===
Dr. Jim Maas
Research Associate in Network Meta-Analysis
School of Medicine, Health Policy and Practice
CD Annex, Room 1.04
University of East Anglia
Norwich, UK
NR4 7TJ
+44 (0) 1603 591412
--
Ivan CALANDRA
PhD Student
University of Hamburg
Biozentrum Grindel und Zoologisches Museum
Abt. Säugetiere
Martin-Luther-King-Platz 3
D-20146 Hamburg, GERMANY
+49(0)40 42838 6231
ivan.calan...@uni-hamburg.de
**
http://www.for771.uni-bonn.de
http://webapp5.rrz.uni-hamburg.de/mammals/eng/mitarbeiter.php
[[alternative HTML version deleted]]
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Re: [R] Interpolate? a line
I think that's because of your definition for touches. If I read it correctly, David's code assumes that a cell is a square 1 unit wide and then followed the normal geometric definition of touches, ie. the line intersects with at least one point on the cell's boundary. You seem to have a different definition: cell centers perhaps ? or cell lower-left corner points ? Whether or not any particular definition is valid depends on your requirements. In other words - it's all up to you :) Michael On 17 September 2010 21:22, Alaios ala...@yahoo.com wrote: I would like to thank you again for your help. But it seems that the floor function (ceiling, round too) create more dots in the matrix that line really touches. unique( floor( cbind( seq(2,62, by=0.1), linefn(seq(2,62, by=0.1)) ) ) ) You can see that in the picture below http://yfrog.com/5blineswj So, how to select the only the cells that the line touches? I would like to thank you in advance for your help best Regards Alex From: David Winsemius dwinsem...@comcast.net Cc: Rhelp list r-help@r-project.org Sent: Wed, September 15, 2010 1:55:10 PM Subject: Re: [R] Interpolate? a line On Sep 15, 2010, at 7:24 AM, David Winsemius wrote: Replacing context: Hello everyone. I have created a 100*100 matrix in R. Let's now say that I have a line that starts from (2,3) point and ends to the (62,34) point. In other words this line starts at cell (2,3) and ends at cell (62,34). Is it possible to get by some R function all the matrix's cells that this line transverses? I would like to thank you for your feedback. Best Regards Alex On Sep 15, 2010, at 6:52 AM, Michael Bedward wrote: Hello Alex, Here is one way to do it. It works but it's not pretty :) If you want an alternative, consider that produces the Y cell indices (since the x cell indices are already 2:62): linefn - function(x) 3+((34-3)/(62-2)) *(x-2) findInterval(linefn(2:62), 3:34) [1] 1 1 2 2 3 3 4 4 5 5 6 6 7 7 8 8 9 9 10 10 11 11 12 12 13 13 14 [28] 14 15 15 16 17 17 18 18 19 19 20 20 21 21 22 22 23 23 24 24 25 25 26 26 27 27 28 [55] 28 29 29 30 30 31 32 # that seems off by two linefn(62) [1] 34 linefn(2) [1] 3 # but that checks out and I realized those were just indices for the 3:34 findInterval vector (3:34)[findInterval(linefn(2:62), 3:34)] [1] 3 3 4 4 5 5 6 6 7 7 8 8 9 9 10 10 11 11 12 12 13 13 14 14 15 15 16 [28] 16 17 17 18 19 19 20 20 21 21 22 22 23 23 24 24 25 25 26 26 27 27 28 28 29 29 30 [55] 30 31 31 32 32 33 34 ( no rounding and I think the logic is clearer.) But I also realized it didn't enumerate all the the cells were crossed either, only indicating which cell was associated with an integer value of x. Also would have even more serious problems if the slope were greater than unity. To enumerate the cell indices that were crossed, try: unique( floor( cbind( seq(2,62, by=0.1), linefn(seq(2,62, by=0.1)) ) ) ) [,1] [,2] [1,] 2 3 [2,] 3 3 [3,] 4 4 [4,] 5 4 [5,] 5 5 [6,] 6 5 [7,] 7 5 [8,] 7 6 snipping interior results [83,] 58 32 [84,] 59 32 [85,] 60 32 [86,] 60 33 [87,] 61 33 [88,] 62 34 That could probably be passed to rect() to illustrate (and check logic): rect(cellidxs[,1], cellidxs[,2], cellidxs[,1]+1, cellidxs[,2]+1, col=red) #redraw line : lines(2:62, 3+(34-3)/(62-2)*(0:60)) --David. interp - approx(c(2, 62), c(3, 34), method=linear, xout=2:62) m - matrix(c(interp$x, round(interp$y)), ncol=2) tie - m[,2] == c(-Inf, m[-nrow(m),2]) m - m[ !tie, ] You might want to examine the result like this... plot(m) # plots points lines(c(2,26), c(3, 34)) # overlay line for comparison you can add a grid with abline(v=2:62, h=3:34) Michael __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. David Winsemius, MD West Hartford, CT __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. David Winsemius, MD West Hartford, CT [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the
Re: [R] Odp: Programming: loop versus vector oriented
Hi Jan Jan private jrheinlaen...@gmx.de napsal dne 17.09.2010 12:43:40: Hello Petr, but I think this is how your code really works. Did you try it? it does, but the R documentation says somewhere: Warning: for() loops are used in R code much less often than in compiled languages. Code that takes a `whole object' view is likely to be both clearer and faster in R. Yes and no. Try to go through R-Inferno from Patrick Burns. For loop is not necessarily slower if properly used. Your problem was specified not very clearly because only in last mail you presented that what you have is 2 equal length vectors which shall give result of the same length. The problem is that (if I remember correctly as I do not keep original mails) you have 3 distinct computations based on values in vector1. So if you want some vectorised computation you has to use either switch or ifelse or cycle. However it is not necessary to do computation one by one as in your function but only 3 times based on threshold criteria. I would do something like: 1. make 3 distinct separate functions which compute relevant values from 2 vectors in a list 2. split vectors according to thresholds to list see ?split 3. make cycle in which for each part of list proper function is used something like }not very elegant. for (i in 1:3) result[[1]] - if (i==1) fun1(mylist1[[i]], mylist2[[1]]) else if(i==2) fun2(mylist1[[i]], ylist2[[1]]) else fun3(mylist1[[i]], ylist2[[1]]) 4. reconstruct result in original vector e.g. cbind(unlist(mylist1), unlist(mylist2), unlist(result)) Regards Petr So I am wondering in what way the whole object view could be applied to my function. Best regards, Jan The function should work on the nth elements of the two input vectors and put the result into the nth element of the output vector. So it would work like c - a + b, only instead of '+' there are more complex calculations. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] count frequency
Hello everyone, please consider the following lines of a matrix [574,] 59 32 [575,] 59 32 [576,] 59 32 [577,] 59 32 [578,] 59 32 [579,] 59 32 [580,] 59 32 [581,] 60 32 [582,] 60 33 [583,] 60 33 [584,] 60 33 [585,] 60 33 [586,] 60 33 [587,] 60 33 [588,] 60 33 [589,] 60 33 [590,] 60 33 [591,] 61 33 [592,] 61 33 [593,] 61 33 [594,] 61 33 [595,] 61 33 [596,] 61 33 [597,] 61 33 [598,] 61 33 [599,] 61 33 [600,] 61 33 [601,] 62 34 Is it possible somehow to count the similarities between the first and second column and put them on a third column like this? 59 32 3 60 33 5 62 34 1 where (3,5,1 are the frequencies for (59,32), (60,33) and (62,34) Best Regards Alex [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] count frequency
-BEGIN PGP SIGNED MESSAGE- Hash: SHA1 On 17/09/10 14:19, Alaios wrote: Hello everyone, please consider the following lines of a matrix [574,] 59 32 [575,] 59 32 [576,] 59 32 [577,] 59 32 [578,] 59 32 [579,] 59 32 [580,] 59 32 [581,] 60 32 [582,] 60 33 [583,] 60 33 [584,] 60 33 [585,] 60 33 [586,] 60 33 [587,] 60 33 [588,] 60 33 [589,] 60 33 [590,] 60 33 [591,] 61 33 [592,] 61 33 [593,] 61 33 [594,] 61 33 [595,] 61 33 [596,] 61 33 [597,] 61 33 [598,] 61 33 [599,] 61 33 [600,] 61 33 [601,] 62 34 Is it possible somehow to count the similarities between the first and second column and put them on a third column like this? 59 32 3 60 33 5 62 34 1 where (3,5,1 are the frequencies for (59,32), (60,33) and (62,34) One solution: x - data.frame(a=trunc(runif(10)*10), b=trunc(runif(10)*10)) x a b 1 6 5 2 7 5 3 1 5 4 0 4 5 3 9 6 6 8 7 4 3 8 0 4 9 2 7 10 7 2 x$comb - paste(x$a, x$b) x a b comb 1 6 5 6 5 2 7 5 7 5 3 1 5 1 5 4 0 4 0 4 5 3 9 3 9 6 6 8 6 8 7 4 3 4 3 8 0 4 0 4 9 2 7 2 7 10 7 2 7 2 table(x$comb) 0 4 1 5 2 7 3 9 4 3 6 5 6 8 7 2 7 5 2 1 1 1 1 1 1 1 1 I am sure, there are better ones Cheers, Rainer Best Regards Alex [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. - -- Rainer M. Krug, PhD (Conservation Ecology, SUN), MSc (Conservation Biology, UCT), Dipl. Phys. (Germany) Centre of Excellence for Invasion Biology Natural Sciences Building Office Suite 2039 Stellenbosch University Main Campus, Merriman Avenue Stellenbosch South Africa Tel:+33 - (0)9 53 10 27 44 Cell: +27 - (0)8 39 47 90 42 Fax (SA): +27 - (0)8 65 16 27 82 Fax (D) : +49 - (0)3 21 21 25 22 44 Fax (FR): +33 - (0)9 58 10 27 44 email: rai...@krugs.de Skype: RMkrug -BEGIN PGP SIGNATURE- Version: GnuPG v1.4.10 (GNU/Linux) Comment: Using GnuPG with Mozilla - http://enigmail.mozdev.org/ iEYEARECAAYFAkyTXoQACgkQoYgNqgF2egrgrgCfUOvMaUOwOC7HPSdbC2fFzdLo 4scAmwQ2M1E000PH4HoQmkpkLbANtjLy =B2y8 -END PGP SIGNATURE- __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Odp: Programming: loop versus vector oriented
Hello Petr, but I think this is how your code really works. Did you try it? it does, but the R documentation says somewhere: Warning: for() loops are used in R code much less often than in compiled languages. Code that takes a `whole object' view is likely to be both clearer and faster in R. So I am wondering in what way the whole object view could be applied to my function. Best regards, Jan The function should work on the nth elements of the two input vectors and put the result into the nth element of the output vector. So it would work like c - a + b, only instead of '+' there are more complex calculations. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] count frequency
Try this: aggregate(rep(1, nrow(x)), x, sum) On Fri, Sep 17, 2010 at 9:19 AM, Alaios ala...@yahoo.com wrote: Hello everyone, please consider the following lines of a matrix [574,] 59 32 [575,] 59 32 [576,] 59 32 [577,] 59 32 [578,] 59 32 [579,] 59 32 [580,] 59 32 [581,] 60 32 [582,] 60 33 [583,] 60 33 [584,] 60 33 [585,] 60 33 [586,] 60 33 [587,] 60 33 [588,] 60 33 [589,] 60 33 [590,] 60 33 [591,] 61 33 [592,] 61 33 [593,] 61 33 [594,] 61 33 [595,] 61 33 [596,] 61 33 [597,] 61 33 [598,] 61 33 [599,] 61 33 [600,] 61 33 [601,] 62 34 Is it possible somehow to count the similarities between the first and second column and put them on a third column like this? 59 32 3 60 33 5 62 34 1 where (3,5,1 are the frequencies for (59,32), (60,33) and (62,34) Best Regards Alex [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. -- Henrique Dallazuanna Curitiba-Paraná-Brasil 25° 25' 40 S 49° 16' 22 O [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] count frequency
On 17-Sep-10 12:19:10, Alaios wrote: Hello everyone, please consider the following lines of a matrix [574,] 59 32 [575,] 59 32 [576,] 59 32 [577,] 59 32 [578,] 59 32 [579,] 59 32 [580,] 59 32 [581,] 60 32 [582,] 60 33 [583,] 60 33 [584,] 60 33 [585,] 60 33 [586,] 60 33 [587,] 60 33 [588,] 60 33 [589,] 60 33 [590,] 60 33 [591,] 61 33 [592,] 61 33 [593,] 61 33 [594,] 61 33 [595,] 61 33 [596,] 61 33 [597,] 61 33 [598,] 61 33 [599,] 61 33 [600,] 61 33 [601,] 62 34 Is it possible somehow to count the similarities between the first and second column and put them on a third column like this? 59 32 3 60 33 5 62 34 1 where (3,5,1 are the frequencies for (59,32), (60,33) and (62,34) Best Regards Alex Does the following do what you want? a - c(59,59,59,59,59,59,59,60,60,60,60,60,60,60, 60,60,60,61,61,61,61,61,61,61,61,61,61,62) b - c(32,32,32,32,32,32,32,32,33,33,33,33,33,33, 33,33,33,33,33,33,33,33,33,33,33,33,33,34) table(data.frame(a=a,b=b)) # b # a32 33 34 # 59 7 0 0 # 60 1 9 0 # 61 0 10 0 # 62 0 0 1 T - t(as.matrix(table(data.frame(a=a,b=b L - c(table(data.frame(a=a,b=b))) B - as.integer(rep(rownames(T),each=ncol(T))) A - as.integer(rep(colnames(T),nrow(T))) cbind(A,B,L)[L0,] # A B L # [1,] 59 32 7 # [2,] 60 32 1 # [3,] 60 33 9 # [4,] 61 33 10 # [5,] 62 34 1 Ted. E-Mail: (Ted Harding) ted.hard...@manchester.ac.uk Fax-to-email: +44 (0)870 094 0861 Date: 17-Sep-10 Time: 14:15:03 -- XFMail -- __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] ifelse statement
Dear list, I have a question I'm trying to use the following command in R, but it gives me an error message.The command is: data-ddply(data,c(year,name), transform, check1=ifelse(check1==1 check2==1, 1,NULL)) so in my data frame I already have the check1 variable, if the conditions (check1==1 check2==1) is respected, check has to have 1 as value, whereas if it is not I want that variable to maintain its value. Anyone knows, how to do this, by doing this for name and year?? __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Survival Analysis Daily Time-Varying Covariate....
Help! I am unsure if I can analyze data from the following experiment. Fish were placed in a tank at (t=0) Measurements of Carbon Dioxide were taken each day for 120 days (t=0,...120) A few fish were then randomly pulled out of the tank at different days, killed and examined for the presence of a disease T= time of examination in days from start (i.e. 85th day), E = 0/1 for nonevent/event --- You need to decide on a mechanistic model. On the day a fish is sacrificed, does their risk of disease depend on today's CO2 level the average CO2 since the start of the experiment cumulative CO2 dose days over a threshold etc You can examine each of these one by one or in combinations. It would be very difficult, however, to ask your program to find the pattern. Terry Therneau __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] ifelse statement
Hi, Not sure since I've never done it, but shouldn't it be NA instead of NULL? Ivan Le 9/17/2010 15:23, n.via...@libero.it a écrit : Dear list, I have a question I'm trying to use the following command in R, but it gives me an error message.The command is: data-ddply(data,c(year,name), transform, check1=ifelse(check1==1 check2==1, 1,NULL)) so in my data frame I already have the check1 variable, if the conditions (check1==1 check2==1) is respected, check has to have 1 as value, whereas if it is not I want that variable to maintain its value. Anyone knows, how to do this, by doing this for name and year?? __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. -- Ivan CALANDRA PhD Student University of Hamburg Biozentrum Grindel und Zoologisches Museum Abt. Säugetiere Martin-Luther-King-Platz 3 D-20146 Hamburg, GERMANY +49(0)40 42838 6231 ivan.calan...@uni-hamburg.de ** http://www.for771.uni-bonn.de http://webapp5.rrz.uni-hamburg.de/mammals/eng/mitarbeiter.php [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] test to see if a s4 property is assigned?
setClass(person,representation(name=character,age=numeric,kids=list)) [1] person bob - new(person) length(b...@name) [1] 0 length(b...@age) [1] 0 length(b...@kids) [1] 0 is.na(b...@kids) logical(0) is.na(b...@age) logical(0) is.na(b...@name) logical(0) b...@kids - list(joe,sue) is.na(b...@kids) [1] FALSE FALSE length(b...@kids) [1] 2 Ah, length(obj...@property) is what i was looking for. Thanks alot. -- View this message in context: http://r.789695.n4.nabble.com/test-to-see-if-a-s4-property-is-assigned-tp2541044p2543895.html Sent from the R help mailing list archive at Nabble.com. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] count frequency
Alaios, Try as.data.frame(table(x[,1], x[,2)) where x is your matrix. HTH, Jorge On Fri, Sep 17, 2010 at 8:19 AM, Alaios wrote: Hello everyone, please consider the following lines of a matrix [574,] 59 32 [575,] 59 32 [576,] 59 32 [577,] 59 32 [578,] 59 32 [579,] 59 32 [580,] 59 32 [581,] 60 32 [582,] 60 33 [583,] 60 33 [584,] 60 33 [585,] 60 33 [586,] 60 33 [587,] 60 33 [588,] 60 33 [589,] 60 33 [590,] 60 33 [591,] 61 33 [592,] 61 33 [593,] 61 33 [594,] 61 33 [595,] 61 33 [596,] 61 33 [597,] 61 33 [598,] 61 33 [599,] 61 33 [600,] 61 33 [601,] 62 34 Is it possible somehow to count the similarities between the first and second column and put them on a third column like this? 59 32 3 60 33 5 62 34 1 where (3,5,1 are the frequencies for (59,32), (60,33) and (62,34) Best Regards Alex [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] Problems creating a Panel
Dear Felipe,
maybe the data (which I can't see through the digest) do not have
variability, maybe something else.
Try sending me the data.frame, I'll see what happens.
Giovanni
--
Message: 72
Date: Thu, 16 Sep 2010 11:49:19 -0500
From: Luis Felipe Parra felipe.pa...@quantil.com.co
To: r-help@r-project.org
Subject: [R] Problems creating a Panel
Message-ID:
aanlktimnvuq8jcu=vesa6s7gr9tqn1bi9tf0xu3ok...@mail.gmail.com
Content-Type: text/plain; charset=iso-8859-1
Hello, I am trying to create a panel with the attached data frame. using
the
following code:
PanelRio = DataRiopaila[which(duplicated(DataRiopaila$SEC_STE)==T),]
PanelRio=plm.data(PanelRio,index=c(SEC_STE,FechaSiembra))
series
Pluv3Meses,PluvMes4al10,Pluv2UltimosMeses,Rad3Meses,RadMes4al10,Rad2Ulti
mosMeses
are NA and have been removed
It tells me it removes couple of series because they are NA, and I don't
understand why because if I do:
PanelRio = DataRiopaila[which(duplicated(DataRiopaila$SEC_STE)==T),]
length(which(is.na(PanelRio[,Pluv3Meses])==T))
[1] 474
nrow(PanelRio)
[1] 4129
which means there are still around 3500 entries which aren't NA. Does
anybody what can be going on?
Thank you
Felipe Parra
---
Giovanni Millo
Research Dept.,
Assicurazioni Generali SpA
Via Machiavelli 4,
34132 Trieste (Italy)
tel. +39 040 671184
fax +39 040 671160
Ai sensi del D.Lgs. 196/2003 si precisa che le informazi...{{dropped:13}}
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Re: [R] count frequency
Just to confirm, this one worked for me as.data.frame(table(temp[])) Var1 Freq 1 1 11 2 2 29 3 3 29 4 4 29 5 5 29 6 6 29 7 7 29 8 8 29 9 9 29 10 10 29 11 11 29 12 12 29 13 13 29 14 14 29 15 15 29 16 16 29 17 17 29 18 18 30 19 19 29 20 20 29 Best Regards Alex From: Jorge Ivan Velez jorgeivanve...@gmail.com Cc: Rhelp r-help@r-project.org Sent: Fri, September 17, 2010 4:24:59 PM Subject: Re: [R] count frequency Alaios, Try as.data.frame(table(x[,1], x[,2)) where x is your matrix. HTH, Jorge On Fri, Sep 17, 2010 at 8:19 AM, Alaios wrote: Hello everyone, please consider the following lines of a matrix [574,] 59 32 [575,] 59 32 [576,] 59 32 [577,] 59 32 [578,] 59 32 [579,] 59 32 [580,] 59 32 [581,] 60 32 [582,] 60 33 [583,] 60 33 [584,] 60 33 [585,] 60 33 [586,] 60 33 [587,] 60 33 [588,] 60 33 [589,] 60 33 [590,] 60 33 [591,] 61 33 [592,] 61 33 [593,] 61 33 [594,] 61 33 [595,] 61 33 [596,] 61 33 [597,] 61 33 [598,] 61 33 [599,] 61 33 [600,] 61 33 [601,] 62 34 Is it possible somehow to count the similarities between the first and second column and put them on a third column like this? 59 32 3 60 33 5 62 34 1 where (3,5,1 are the frequencies for (59,32), (60,33) and (62,34) Best Regards Alex [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Can I save my console contents automatically?
Hello Greg, Thank you for your comment. I had a chance to use Windows GUI R and I found several interesting differences between Mac and Windows GUI R. 1. txtStart() command - Windows GUI R - worked perfectly - Mac GUI R version.string R version 2.11.1 (2010-05-31) (both 32bit and 64bit) - only make a null file - Mac R version.string R version 2.11.1 (2010-05-31) on terminal window - worked perfectly (I also checked the permissions, but they were OK.) 2. Console - Mac GUI R can display very long results and can save them from the file menu (manually). - Windows GUI R can only short results and can save only the displayed results from the file menu. 3. sink() - Mac GUI R - split = TRUE worked. - Windows GUI R -split = TRUE didn't work (log on the file, but didn't display the results on the console). Thanks. Nobu Currently comments (#) are ignored by txtStart and friends due to the task callback mechanism used. The txtComment function is available as a work around to insert comments into the output/commands. I tried running date() as below and everything worked as expected (the comments were missing, but the date command and result were in the file. I am running on windows where it looks like you are running on unix or linux. Can you send your OS and version of R and TeachingDemos? Also what are the permissions on the logtest.txt file that is created? (I've seen problems where the permissions for a directory allowed the creating of a file, but the default permissions on the file then do not allow modification). -- Gregory (Greg) L. Snow Ph.D. Statistical Data Center Intermountain Healthcare greg.s...@imail.org 801.408.8111 -Original Message- From: r-help-boun...@r-project.org [mailto:r-help-boun...@r- project.org] On Behalf Of Nobuaki Michihata Sent: Thursday, September 16, 2010 8:24 AM To: r-help Subject: Re: [R] Can I save my console contents automatically? Hello David and Greg, Thank you for your suggestions. These really help me. I'm curious about txtStart function of TeachingDemos library. It looks exactly what I need. So I installed TeachingDemos library and tried following. - library(TeachingDemos) setwd(/Users/NOBU/Documents/R_data/) txtStart(logtest.txt, commands = TRUE, results = TRUE, append = FALSE) #Top of commands date() #End of commands txtStop() --- Then I got following outputs on my console window, but I only got a null file named logtest.txt. I tried several times by trial and error, but I couldn't find the solution to log outputs on the logtest.txt. --- library(TeachingDemos) setwd(/Users/NOBU/Documents/R_data/) txtStart(logtest.txt, commands = TRUE, results = TRUE, append = FALSE) Output being copied to text file, use txtStop to end txt txt #Top of commands txt date() [1] Thu Sep 16 07:16:29 2010 txt #End of commands txt txt txtStop() Thank you for your help! Nobu 2010/9/14 Nobuaki Michihata gha10...@gmail.com: Dear All, I found a following solution from http://r.789695.n4.nabble.com/;. However this command can save only the result. Is there any good solution to save both commands themselves and the results. Thank you for your help. sink(Filename_here.log, type=c(output,message), split=TRUE) # Put commands here # However this method save only the results. sink() Nobu Message: 33 Date: Fri, 10 Sep 2010 07:07:37 -0700 From: Nobuaki Michihata gha10...@gmail.com To: r-help@r-project.org, r-help@r-project.org Subject: [R] Can I save my console contents automatically? Message-ID: AANLkTimEZ-igqK6GzeYqERZaTg7m+chjbGJmAGmEL- y...@mail.gmail.com Content-Type: text/plain; charset=ISO-8859-1 Dear All, I'm using R for Mac OS X Cocoa GUI R version 2.11.1. I can save contents of my console window by using command + s, but I would like to do same thing using R commands. My question is can I save the contents automatically by using R editor with some R commands. Thank you. Nobu __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting- guide.html and provide commented, minimal, self-contained, reproducible code. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] removing specific rows from array
I'm attempting to create an array of treatment comparisons for modelling data generation. This involves comparison of one treatment (c2) with another (c3), relative to a common comparator (c1). Attached code gives me the correct array but need to remove duplicates. Duplicates relate only to c2 and c3 such that I need to remove r3 because c2 and c3 are same as r1 with c2 and c3 swapped r5 because c2 and c3 are same as r2 with c2 and c3 swapped r6 because c2 and c3 are same as r4 with c2 and c3 swapped r9 because c2 and c3 are same as r7 with c2 and c3 swapped r11 because c2 and c3 are same as r8 with c2 and c3 swapped . . . Any suggestions? Thanks Jim treats - c(t0,t1,t2,t3) (combs1 - permutations(length(treats),3,treats)) [,1] [,2] [,3] [1,] t0 t1 t2 [2,] t0 t1 t3 [3,] t0 t2 t1 [4,] t0 t2 t3 [5,] t0 t3 t1 [6,] t0 t3 t2 [7,] t1 t0 t2 [8,] t1 t0 t3 [9,] t1 t2 t0 [10,] t1 t2 t3 [11,] t1 t3 t0 [12,] t1 t3 t2 [13,] t2 t0 t1 [14,] t2 t0 t3 [15,] t2 t1 t0 [16,] t2 t1 t3 [17,] t2 t3 t0 [18,] t2 t3 t1 [19,] t3 t0 t1 [20,] t3 t0 t2 [21,] t3 t1 t0 [22,] t3 t1 t2 [23,] t3 t2 t0 [24,] t3 t2 t1 === Dr. Jim Maas University of East Anglia __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] using variable from for loop in naming new variables
On Fri, Sep 17, 2010 at 4:46 AM, Ivan Calandra
ivan.calan...@uni-hamburg.de wrote:
Hi Jim,
First, I think it's better if you reply to the list, other users might
be interested and have better answers.
Second, as other replies showed you, using a list is actually way easier
than creating new objects every time. Check especially the reply from
Joshua Wiley, which gives you great examples and guidance.
Last, regarding rm(list=ls()), what's the point of creating new objects
in your loop if you remove them right after?! Maybe you intend to do
stuff on them first. Anyway, I don't use Emacs so not sure why you do it
that way. Just my limited opinion.
HTH,
Ivan
Le 9/17/2010 12:35, Maas James Dr (MED) a écrit :
Hi Ivan,
Thanks for suggestions, was just hoping to do it all in one step,
creating a list and then filling it all seems rather complicated ...
will look up *apply.
I'd be happy to try to help you simplify things, but to offer much
advice we would probably need to know more about your end goal. At
least in the simple example you gave, the one step version is:
as.list(3 + 1:4)
but I am guessing you are not actually interested in that ;-)
As for removing objects, I run R interactively from within Emacs (ESS)
and stuff hangs around for successive evaluations, not sure where it
came from so I clean it out every time ... is there a better way?
That will be because of the .Rhistory file I would think. My
suggestion would be to clean it out once and save (so that its empty),
and from then on whenever you exit just use q(no) or just type q()
and R should ask you whether you want to save the workspace image and
you can hit n.
The only way I remember how to setup Emacs to not save by default is
to start R using C-u M-x R and then passing the command line
argument --no-save, but honestly that is so lengthy it would just be
easier to clean it out each time. I know there's an easier way but I
never remember it.
Josh
Thanks
Jim
Message: 65
Date: Thu, 16 Sep 2010 18:03:29 +0200
From: Ivan Calandra ivan.calan...@uni-hamburg.de
To: r-help@r-project.org
Subject: Re: [R] using variable from for loop in naming new variables
Message-ID: 4c923fd1.8000...@uni-hamburg.de
Content-Type: text/plain
Hi!
assign() should do the job.
But using a list, and filling each element iteratively (with a for loop
or with *apply() ) might be better, up to you.
Btw, why do you remove your objects?
HTH,
Ivan
Le 9/16/2010 17:44, Maas James Dr (MED) a ?crit :
Simple one here ... but can't get it to work ...
for (i in 1:4){
paste(stuff,[i]),sep=)- 3 + i
}
ls()
rm(list=ls())
I just want it to create 4 new variables called stuff1, stuff2,
stuff3, stuff4 with the corresponding assignments. I realise that
there are more elegant functions but this is just a model of a bigger
situation.
Thanks
Jim
===
Dr. Jim Maas
Research Associate in Network Meta-Analysis
School of Medicine, Health Policy and Practice
CD Annex, Room 1.04
University of East Anglia
Norwich, UK
NR4 7TJ
+44 (0) 1603 591412
--
Ivan CALANDRA
PhD Student
University of Hamburg
Biozentrum Grindel und Zoologisches Museum
Abt. Säugetiere
Martin-Luther-King-Platz 3
D-20146 Hamburg, GERMANY
+49(0)40 42838 6231
ivan.calan...@uni-hamburg.de
**
http://www.for771.uni-bonn.de
http://webapp5.rrz.uni-hamburg.de/mammals/eng/mitarbeiter.php
[[alternative HTML version deleted]]
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Ph.D. Student, Health Psychology
University of California, Los Angeles
http://www.joshuawiley.com/
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Re: [R] count frequency
My bad :( unfortunately does not work correct. This is some of the output of the table .. [494,] 50 27 [495,] 50 27 [496,] 50 27 [497,] 50 28 [498,] 50 28 [499,] 50 28 [500,] 50 28 [501,] 51 28 [502,] 51 28 [503,] 51 28 [504,] 51 28 [505,] 51 28 [506,] 51 28 [507,] 51 28 [508,] 51 28 [509,] 51 28 [510,] 51 28 [511,] 52 28 [512,] 52 28 [513,] 52 28 [514,] 52 28 [515,] 52 28 [516,] 52 29 [517,] 52 29 [518,] 52 29 I need the following results 50 27: 3 50 28: 4 51 28: 10 52 28: 5 52 29: 3 So far nothing worked. Best Regards Alex From: Henrique Dallazuanna www...@gmail.com Cc: Rhelp r-help@r-project.org Sent: Fri, September 17, 2010 3:09:36 PM Subject: Re: [R] count frequency Try this: aggregate(rep(1, nrow(x)), x, sum) Hello everyone, please consider the following lines of a matrix [574,] 59 32 [575,] 59 32 [576,] 59 32 [577,] 59 32 [578,] 59 32 [579,] 59 32 [580,] 59 32 [581,] 60 32 [582,] 60 33 [583,] 60 33 [584,] 60 33 [585,] 60 33 [586,] 60 33 [587,] 60 33 [588,] 60 33 [589,] 60 33 [590,] 60 33 [591,] 61 33 [592,] 61 33 [593,] 61 33 [594,] 61 33 [595,] 61 33 [596,] 61 33 [597,] 61 33 [598,] 61 33 [599,] 61 33 [600,] 61 33 [601,] 62 34 Is it possible somehow to count the similarities between the first and second column and put them on a third column like this? 59 32 3 60 33 5 62 34 1 where (3,5,1 are the frequencies for (59,32), (60,33) and (62,34) Best Regards Alex [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. -- Henrique Dallazuanna Curitiba-Paraná-Brasil 25° 25' 40 S 49° 16' 22 O [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] count frequency
So try this : aggregate(rep(1, nrow(x)), as.data.frame(x), sum) On Fri, Sep 17, 2010 at 11:54 AM, Alaios ala...@yahoo.com wrote: My bad :( unfortunately does not work correct. This is some of the output of the table .. [494,] 50 27 [495,] 50 27 [496,] 50 27 [497,] 50 28 [498,] 50 28 [499,] 50 28 [500,] 50 28 [501,] 51 28 [502,] 51 28 [503,] 51 28 [504,] 51 28 [505,] 51 28 [506,] 51 28 [507,] 51 28 [508,] 51 28 [509,] 51 28 [510,] 51 28 [511,] 52 28 [512,] 52 28 [513,] 52 28 [514,] 52 28 [515,] 52 28 [516,] 52 29 [517,] 52 29 [518,] 52 29 I need the following results 50 27: 3 50 28: 4 51 28: 10 52 28: 5 52 29: 3 So far nothing worked. Best Regards Alex -- *From:* Henrique Dallazuanna www...@gmail.com *To:* Alaios ala...@yahoo.com *Cc:* Rhelp r-help@r-project.org *Sent:* Fri, September 17, 2010 3:09:36 PM *Subject:* Re: [R] count frequency Try this: aggregate(rep(1, nrow(x)), x, sum) On Fri, Sep 17, 2010 at 9:19 AM, Alaios ala...@yahoo.com wrote: Hello everyone, please consider the following lines of a matrix [574,] 59 32 [575,] 59 32 [576,] 59 32 [577,] 59 32 [578,] 59 32 [579,] 59 32 [580,] 59 32 [581,] 60 32 [582,] 60 33 [583,] 60 33 [584,] 60 33 [585,] 60 33 [586,] 60 33 [587,] 60 33 [588,] 60 33 [589,] 60 33 [590,] 60 33 [591,] 61 33 [592,] 61 33 [593,] 61 33 [594,] 61 33 [595,] 61 33 [596,] 61 33 [597,] 61 33 [598,] 61 33 [599,] 61 33 [600,] 61 33 [601,] 62 34 Is it possible somehow to count the similarities between the first and second column and put them on a third column like this? 59 32 3 60 33 5 62 34 1 where (3,5,1 are the frequencies for (59,32), (60,33) and (62,34) Best Regards Alex [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. -- Henrique Dallazuanna Curitiba-Paraná-Brasil 25° 25' 40 S 49° 16' 22 O -- Henrique Dallazuanna Curitiba-Paraná-Brasil 25° 25' 40 S 49° 16' 22 O [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] function help?
On 9/16/10 5:00 PM, Rolf Turner wrote: On 17/09/2010, at 8:51 AM, Duke wrote: Hi Duncan, On 9/16/10 3:47 PM, Duncan Murdoch wrote: On 16/09/2010 3:40 PM, Duke wrote: Hi all, I am writing a function (fun.R), but I dont know how to code the function so that the Help Text will be shown up when one types ?fun (of course, after he loads it up). Anyone has any advice for me how to do that? The help text is separate from the function (unless you use the roxygen package or similar). You need to write a package so that R will find the help; instructions are in the Writing R Extensions manual. I was expecting something simpler than writing a package, and that I can integrate it into fun.R, but thanks anyway. (a) Writing a package is not all that hard. You can say so if you are fluent in R. I just started and have written only 20-30 lines of codes so far. Also, writing a package is still more complicated than writing a simple function (single file). Why R is so different from other languages (python, matlab or more basics like C/C++ etc...)? In fact I still feel very uncomfortable with R, for example, I hate when I type a function name, it shows the whole function. Honestly I feel a world of programming is a mess, and it is tough when one wants to jump from one language to another. (b) It focuses the mind wondrously. I did try to write a simple package (followed a tutorial), but did not find what you said :). Maybe I need more practice. (c) Using R CMD check on the package is very useful for picking the lint off the code. It would be great if you share your experience a little more about this. Thanks, D. cheers, Rolf Turner ## Attention: This e-mail message is privileged and confidential. If you are not the intended recipient please delete the message and notify the sender. Any views or opinions presented are solely those of the author. This e-mail has been scanned and cleared by MailMarshal www.marshalsoftware.com ## __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] question on OPTIMX with installing and using
Dear R users
I have tried to install the optimx but met problems.
I have gone to the website you suggested:
https://r-forge.r-project.org/R/?group_id=395
and tried to install it with the following method:
install.packages(optimx, repos=http://R-Forge.R-project.org;)
I have received the following information:
package 'numDeriv' successfully unpacked and MD5 sums checked
package 'BB' successfully unpacked and MD5 sums checked
package 'ucminf' successfully unpacked and MD5 sums checked
package 'Rcgmin' successfully unpacked and MD5 sums checked
package 'Rvmmin' successfully unpacked and MD5 sums checked
package 'minqa' successfully unpacked and MD5 sums checked
package 'setRNG' successfully unpacked and MD5 sums checked
package 'optimx' successfully unpacked and MD5 sums checked
The downloaded packages are in
C:\Documents and Settings\mycomputer\Local
Settings\Temp\Rtmpd7resh\downloaded_packages
after that, I have tried the following example from the manual of optimx but
encountered error message as:
Error: could not find function optimx
after that I have tried download the package for windows, optimx_0.86.zip, and
all other support routines, installed them from the menu of install package
from local zip file. but i still met the upper error message.
I then use: library(optimx) this loaded the optimx, I think, but the
optansout has been masked by Rvmmin and Rcgmin. then when I tried the
following example, the error message shows:
Error: package 'tools' does not have a name space
any suggestions for the question on the upper two parts? any suggestion are
apprecitated
Nan
from Montreal
Example code from optimx manual:
require(graphics)
fr - function(x) { ## Rosenbrock Banana function
x1 - x[1]
x2 - x[2]
100 * (x2 - x1 * x1)^2 + (1 - x1)^2
}
grr - function(x) { ## Gradient of 'fr'
x1 - x[1]
x2 - x[2]
c(-400 * x1 * (x2 - x1 * x1) - 2 * (1 - x1),
200 * (x2 - x1 * x1))
}
ans1-optimx(c(-1.2,1), fr)
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Re: [R] count frequency
You are pretty good. Worked nicely :) Thanks! Alex From: Henrique Dallazuanna www...@gmail.com Cc: Rhelp r-help@r-project.org Sent: Fri, September 17, 2010 4:58:50 PM Subject: Re: [R] count frequency So try this : aggregate(rep(1, nrow(x)), as.data.frame(x), sum) My bad :( unfortunately does not work correct. This is some of the output of the table .. [494,] 50 27 [495,] 50 27 [496,] 50 27 [497,] 50 28 [498,] 50 28 [499,] 50 28 [500,] 50 28 [501,] 51 28 [502,] 51 28 [503,] 51 28 [504,] 51 28 [505,] 51 28 [506,] 51 28 [507,] 51 28 [508,] 51 28 [509,] 51 28 [510,] 5128 [511,] 52 28 [512,] 52 28 [513,] 52 28 [514,] 52 28 [515,] 52 28 [516,] 52 29 [517,] 52 29 [518,] 52 29 I need the following results 50 27: 3 50 28: 4 51 28: 10 52 28: 5 52 29: 3 So far nothing worked. Best Regards Alex From: Henrique Dallazuanna www...@gmail.com Cc: Rhelp r-help@r-project.org Sent: Fri, September 17, 2010 3:09:36 PM Subject: Re: [R] count frequency Try this: aggregate(rep(1, nrow(x)), x, sum) Hello everyone, please consider the following lines of a matrix [574,] 59 32 [575,] 59 32 [576,] 59 32 [577,] 59 32 [578,] 59 32 [579,] 59 32 [580,] 59 32 [581,] 60 32 [582,] 60 33 [583,] 60 33 [584,] 60 33 [585,] 60 33 [586,] 60 33 [587,] 60 33 [588,] 60 33 [589,] 60 33 [590,] 60 33 [591,] 61 33 [592,] 61 33 [593,] 61 33 [594,] 61 33 [595,] 61 33 [596,] 61 33 [597,] 61 33 [598,] 61 33 [599,] 61 33 [600,] 61 33 [601,] 62 34 Is it possible somehow to count the similarities between the first and second column and put them on a third column like this? 59 32 3 60 33 5 62 34 1 where (3,5,1 are the frequencies for (59,32), (60,33) and (62,34) Best Regards Alex [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. -- Henrique Dallazuanna Curitiba-Paraná-Brasil 25° 25' 40 S 49° 16' 22 O -- Henrique Dallazuanna Curitiba-Paraná-Brasil 25° 25' 40 S 49° 16' 22 O [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] Voting power indices
Dear R-experts, I was wondering if anyone know of a library in R that has functions for calculating the Banzhaf and Shaply-Shubik indeces? Best, Thomas __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Combining Data Sets w/ Weights
Here it is... str(Males$BMXHT) num [1:2801] 168 161 180 182 169 ... str(Females$BMXHT) num [1:3440] 162 159 164 165 159 ... str(Males$yourWeight) num [1:2801] 1148 788 10298 25115 8691 ... str(Females$myWeight) num [1:3440] 9169 4964 2608 2806 907 ... I want to combine Males$BMXHT with Females$BMXHT. I also want to combine Males$yourWeight and Females$myWeight in a similar way so that I can use the wtd.quantile() command in the following way: wtd.quantile(Everybody$BMXHT, weights=ourWeight, 0.05) I know that this might seem like some elementary stuff, but I'm not too familiar with R yet. I hope to become much better in the future. Thanks for all of your help, Brian -- View this message in context: http://r.789695.n4.nabble.com/Combining-Data-Sets-w-Weights-tp2543167p2543995.html Sent from the R help mailing list archive at Nabble.com. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] How to find STRESS criteria in MDS when there are negative eigenvalues....
Hi,
I want to know whether there is any function in R to find STRESS after using
cmdscale and estimating the coordinates, I have written these functions to find
stress (for p =1,2,3,4,5)
stress-rep(0,5)
for(p in 1:5)
{
datahat-cmdscale(d,p)
deltahat-as.matrix(dist(datahat))
a-0
b-0
for(i in 1:n)
{
for(j in 1:n)
{
a-d[i,j]^2+a
b-(d[i,j]-deltahat[i,j])^2+b
}
}
stress[p]-b/a
}
stress-sqrt(stress)
stress
but it seems that it is not true when there are negative eigenvalues in
dissimilarity matrix could you please help me to find the answer
thank you in anticipation
[[alternative HTML version deleted]]
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Re: [R] Combining Data Sets w/ Weights
Sorry, Rather, it should be: wtd.quantile(Everybody$BMXHT, weights=Everybody$ourWeight, 0.05) Thanks again, Brian. -- View this message in context: http://r.789695.n4.nabble.com/Combining-Data-Sets-w-Weights-tp2543167p2543998.html Sent from the R help mailing list archive at Nabble.com. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] Unresolves symbol in libR.so
Hello,
I am having a problem configuring a Redhat server to run R as a shared library
called from Perl.
The error message I get is:
Can't find 'boot_R' symbol in libR.so
Has anyone run across something similar?
Any help would be greatly appreciated.
Thank you,
Kenneth Buck
Emory Winship Cancer Institute
This e-mail message (including any attachments) is for t...{{dropped:14}}
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[R] Is there a project to compile R scripts into stand-alone executable file?
I know Matlab's M file can be converted to a stand-alone executable file. I wonder if there is a project aimed at compiling R scripts into stand-alone executable file. I think it will be very promising for R to be more widely used in different fields. -- View this message in context: http://r.789695.n4.nabble.com/Is-there-a-project-to-compile-R-scripts-into-stand-alone-executable-file-tp2544045p2544045.html Sent from the R help mailing list archive at Nabble.com. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] convert to csv file
I get an error message: Error in file(file, ifelse(append, a, w)) : invalid 'open' argument How do I resolve this? -- View this message in context: http://r.789695.n4.nabble.com/convert-to-csv-file-tp2543232p2544070.html Sent from the R help mailing list archive at Nabble.com. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] a reliable way to check the latest version of R on CRAN?
On Thu, Sep 16, 2010 at 5:29 PM, Yihui Xie x...@yihui.name wrote: Hi all, We know old.packages() can check for updates of add-on packages, but is there a way to check updates of R itself? go to R homepage is a way, of course, but I hope this can be done by R. I'm not sure about the reliable place to check; here is a simple example to check from one of the CRAN webpages (kind of nasty approach...): checkRVersion in gtools does it by looking for the .tar.gz releases in CRAN: library(gtools) checkRVersion() A newer version of R is now available: 2.11.1 and then a bit later checkRVersion() The latest version of R is installed: 2.11.1 It returns the latest version and you can make it quiet for use in scripts. Barry __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] Matrix- create mean/min/max/stdev on column of matrix or rows?
I made simulation with Weibull and create Matrix, How can I create mean/min/max/stdev on column or rows of matrix?, Thanks, __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] convert to csv file
More context would be useful, but my first guess is that you are running into problems because both file and append are functions. If you didn't explicitly set them to something else, R is using the function. What happens if you instead use: filename - myfile.csv toappend - FALSE file(filename, ifelse(toappend, a, w)) Sarah On Fri, Sep 17, 2010 at 12:02 PM, lord12 gaut...@yahoo.com wrote: I get an error message: Error in file(file, ifelse(append, a, w)) : invalid 'open' argument How do I resolve this? -- -- Sarah Goslee http://www.functionaldiversity.org __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] convert to csv file
-Original Message- From: r-help-boun...@r-project.org [mailto:r-help-boun...@r-project.org] On Behalf Of lord12 Sent: Friday, September 17, 2010 9:02 AM To: r-help@r-project.org Subject: Re: [R] convert to csv file I get an error message: Error in file(file, ifelse(append, a, w)) : invalid 'open' argument How do I resolve this? More context would help. E.g., what command did you type to get that message? You can get it from sink(junk.txt, append=NULL) Error in file(file, ifelse(append, a, w)) : invalid 'open' argument or sink(junk.txt, append=c(TRUE,FALSE)) Error in file(file, ifelse(append, a, w)) : invalid 'open' argument or sink(junk.txt, append=NA) Error in file(file, ifelse(append, a, w)) : invalid 'open' argument because sink expect append to be either TRUE or FALSE. Bill Dunlap Spotfire, TIBCO Software wdunlap tibco.com -- View this message in context: http://r.789695.n4.nabble.com/convert-to-csv-file-tp2543232p25 44070.html Sent from the R help mailing list archive at Nabble.com. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Interpolate? a line
On Sep 17, 2010, at 7:22 AM, Alaios wrote: I would like to thank you again for your help. But it seems that the floor function (ceiling, round too) create more dots in the matrix that line really touches. You said cells not dots. Are you trying to change the problem now? My concern is rather that it can still miss cells. unique( floor( cbind( seq(2,62, by=0.1), linefn(seq(2,62, by=0.1)) ) ) ) You can see that in the picture below http://yfrog.com/5blineswj So, how to select the only the cells that the line touches? If you had taken my suggestion of overlaying a grid rather than plotting dots that fail to represent a cell (which I was taking to be a square of dimension 1 x 1) you would see that my solution was correct (at least to the point of not missing any cells so defined that were touched up to a tolerance of 0.01 cell units. If you want to define cells differently, then it's your turn to step up and get mathematically precise. Calculus still works if you define neighborhoods as hyperspheres s rather than epsilon by delta hyper- rectangles. # Here is the the illustrated sequence of getting to what I am calling my final answer, # even though it could still miss an occasional cell. interp - approx(c(2, 62), c(3, 34), method=linear, xout=2:62) m - matrix(c(interp$x, round(interp$y)), ncol=2) tie - m[,2] == c(-Inf, m[-nrow(m),2]) m - m[ !tie, ] plot(m) # plots points lines(c(2,62), c(3, 34)) # overlay line for comparison #you can add a grid with abline(v=2:62, h=3:34) ## First attempt at integer values of x linefn - function(x) 3+((34-3)/(62-2)) *(x-2) findInterval(linefn(2:62), 3:34) # Second attempt at 0.1 intervals # cellidxs - unique( floor( cbind( seq(2,62, by=0.1), # There will be many duplicates after rounding down linefn(seq(2,62, by=0.1)) ) ) ) # the same function that just gets a y value rect(cellidxs[,1], cellidxs[,2], cellidxs[,1]+1, cellidxs[,2]+1, col=red) #redraw line : lines(2:62, 3+(34-3)/(62-2)*(0:60)) # That is the first plot with coarse tolerances #Third attempt: # Now calculate a set of cell ids with tolerances that at ten-fold more numerous cellid2 -unique( floor(cbind(seq(2,62, by=0.01), linefn(seq(2,62, by=0.01) )) ) ) NROW(cellid2) # 91 cells rect(cellid2[,1], cellid2[,2], cellid2[,1]+1, cellid2[,2]+1, col=blue) rect(cellidxs[,1], cellidxs[,2], cellidxs[,1]+1, cellidxs[,2]+1, col=red) lines(2:62, 3+(34-3)/(62-2)*(0:60)) -- Best David. I would like to thank you in advance for your help best Regards Alex From: David Winsemius dwinsem...@comcast.net To: Alaios ala...@yahoo.com Cc: Rhelp list r-help@r-project.org Sent: Wed, September 15, 2010 1:55:10 PM Subject: Re: [R] Interpolate? a line On Sep 15, 2010, at 7:24 AM, David Winsemius wrote: Replacing context: Hello everyone. I have created a 100*100 matrix in R. Let's now say that I have a line that starts from (2,3) point and ends to the (62,34) point. In other words this line starts at cell (2,3) and ends at cell (62,34). Is it possible to get by some R function all the matrix's cells that this line transverses? I would like to thank you for your feedback. Best Regards Alex On Sep 15, 2010, at 6:52 AM, Michael Bedward wrote: Hello Alex, Here is one way to do it. It works but it's not pretty :) If you want an alternative, consider that produces the Y cell indices (since the x cell indices are already 2:62): linefn - function(x) 3+((34-3)/(62-2)) *(x-2) findInterval(linefn(2:62), 3:34) [1] 1 1 2 2 3 3 4 4 5 5 6 6 7 7 8 8 9 9 10 10 11 11 12 12 13 13 14 [28] 14 15 15 16 17 17 18 18 19 19 20 20 21 21 22 22 23 23 24 24 25 25 26 26 27 27 28 [55] 28 29 29 30 30 31 32 # that seems off by two linefn(62) [1] 34 linefn(2) [1] 3 # but that checks out and I realized those were just indices for the 3:34 findInterval vector (3:34)[findInterval(linefn(2:62), 3:34)] [1] 3 3 4 4 5 5 6 6 7 7 8 8 9 9 10 10 11 11 12 12 13 13 14 14 15 15 16 [28] 16 17 17 18 19 19 20 20 21 21 22 22 23 23 24 24 25 25 26 26 27 27 28 28 29 29 30 [55] 30 31 31 32 32 33 34 ( no rounding and I think the logic is clearer.) But I also realized it didn't enumerate all the the cells were crossed either, only indicating which cell was associated with an integer value of x. Also would have even more serious problems if the slope were greater than unity. To enumerate the cell indices that were crossed, try: unique( floor( cbind( seq(2,62, by=0.1), linefn(seq(2,62, by=0.1)) ) ) ) [,1] [,2] [1,]23 [2,]33 [3,]44 [4,]54 [5,]55 [6,]65 [7,]75 [8,]76 snipping interior results [83,] 58 32 [84,] 59 32 [85,] 60 32 [86,] 60 33 [87,] 61 33 [88,] 62 34 That could probably be passed to rect() to illustrate (and check logic): rect(cellidxs[,1], cellidxs[,2], cellidxs[,1]+1,
[R] How to include rows with zeros in all columns when clustering data for heatmap?
I am making a heatmap. In the dataset, I have couple of rows with zero value in all the columns. When I cluster data using hierarchical clustering, R gives an error message. When I get rid of those particular rows, the script runs smoothly with no problem. I have to include those rows somehow and also need to cluster the data. Is there a way around to do this? BD -- View this message in context: http://r.789695.n4.nabble.com/How-to-include-rows-with-zeros-in-all-columns-when-clustering-data-for-heatmap-tp2544115p2544115.html Sent from the R help mailing list archive at Nabble.com. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Combining Data Sets w/ Weights
Good News! I think I figured out my problem. The command I was looking for was append(). Thank you for your help, Brian -- View this message in context: http://r.789695.n4.nabble.com/Combining-Data-Sets-w-Weights-tp2543167p2544125.html Sent from the R help mailing list archive at Nabble.com. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] function help?
If having the definition of the function appear when you enter the name of the function elicits a hate response, then perhaps you should not be using R. That characteristic of R is fundamental and unlikely to change: in R everything is an object, and the result of evaluating an expression is displayed at the command line. Other languages have different unifying principles, and may be appropriate for different tasks. Anything that can be done in R could be done in, say, C, but by the time you did so you might find yourself learning very similar lessons to the ones R assumes you know. Duke duke.li...@gmx.com wrote: On 9/16/10 5:00 PM, Rolf Turner wrote: On 17/09/2010, at 8:51 AM, Duke wrote: Hi Duncan, On 9/16/10 3:47 PM, Duncan Murdoch wrote: On 16/09/2010 3:40 PM, Duke wrote: Hi all, I am writing a function (fun.R), but I dont know how to code the function so that the Help Text will be shown up when one types ?fun (of course, after he loads it up). Anyone has any advice for me how to do that? The help text is separate from the function (unless you use the roxygen package or similar). You need to write a package so that R will find the help; instructions are in the Writing R Extensions manual. I was expecting something simpler than writing a package, and that I can integrate it into fun.R, but thanks anyway. (a) Writing a package is not all that hard. You can say so if you are fluent in R. I just started and have written only 20-30 lines of codes so far. Also, writing a package is still more complicated than writing a simple function (single file). Why R is so different from other languages (python, matlab or more basics like C/C++ etc...)? In fact I still feel very uncomfortable with R, for example, I hate when I type a function name, it shows the whole function. Honestly I feel a world of programming is a mess, and it is tough when one wants to jump from one language to another. (b) It focuses the mind wondrously. I did try to write a simple package (followed a tutorial), but did not find what you said :). Maybe I need more practice. (c) Using R CMD check on the package is very useful for picking the lint off the code. It would be great if you share your experience a little more about this. Thanks, D. cheers, Rolf Turner ## Attention: This e-mail message is privileged and confidential. If you are not the intended recipient please delete the message and notify the sender. Any views or opinions presented are solely those of the author. This e-mail has been scanned and cleared by MailMarshal www.marshalsoftware.com ## __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. --- Jeff NewmillerThe . . Go Live... DCN:jdnew...@dcn.davis.ca.usBasics: ##.#. ##.#. Live Go... Live: OO#.. Dead: OO#.. Playing Research Engineer (Solar/BatteriesO.O#. #.O#. with /Software/Embedded Controllers) .OO#. .OO#. rocks...1k --- Sent from my phone. Please excuse my brevity. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Combining Data Sets w/ Weights
On Sep 17, 2010, at 11:15 AM, btpagano wrote: Here it is... str(Males$BMXHT) num [1:2801] 168 161 180 182 169 ... str(Females$BMXHT) num [1:3440] 162 159 164 165 159 ... str(Males$yourWeight) num [1:2801] 1148 788 10298 25115 8691 ... str(Females$myWeight) num [1:3440] 9169 4964 2608 2806 907 ... I want to combine Males$BMXHT with Females$BMXHT. If you have already gone to the trouble of splitting the data into separate male and female dataset (an entirely unnecessary and probably wasteful step I might add) then you can recombine particular vectors with the c() function (c for concatenate). I also want to combine Males$yourWeight and Females$myWeight in a similar way so that I can use the wtd.quantile() command in the following way: wtd.quantile(Everybody$BMXHT, weights=ourWeight, 0.05) I hope you are using the weights argument correctly. You need to be clear about whether these are: sampling weights, frequency weights (which I believe is the correct form for this particular function) or weights in pounds (and that would make no sense but the HT and Weight terminology made me ask). wtd.quantile( c(Males$BMXHT,Females$BMXHT) , weights= c(Males$yourWeight, Females$myWeight), 0.05) If those values had been in the same object with a sex variable, there would have been much more efficient methods available. I know that this might seem like some elementary stuff, but I'm not too familiar with R yet. I hope to become much better in the future. I fear that you have some unlearning of inefficient statistical practices that were taught you in Minitab classes. Thanks for all of your help, Brian -- View this message in context: http://r.789695.n4.nabble.com/Combining-Data-Sets-w-Weights-tp2543167p2543995.html Sent from the R help mailing list archive at Nabble.com. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. David Winsemius, MD West Hartford, CT __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] grouping dataframe entries using a categorical variable
DearR Users, I have a problem which I think you might be able to help. I have a dataframe which I'm trying to filter following different groups I specified. It's a little hard to explain, so here is an example: My dataframe: ESS DHP 1 EPB 22 2 SAB 10 3 SAB 20 4 BOJ 14 5 ERS 28 11 SAB 10 12 SAB 22 13 BOJ 26 20 SAB 10 21 SAB 22 22 BOJ 32 29 SAB 14 30 SAB 22 38 SAB 14 47 SAB 18 I'm trying to filter it by selecting a subgroup of ESS, for example: softwood- c(EPB,SAB) So I can obtain: NEW dataframe: ESS DHP 1 EPB 22 2 SAB 10 3 SAB 20 11 SAB 10 12 SAB 22 20 SAB 10 21 SAB 22 29 SAB 14 30 SAB 22 38 SAB 14 47 SAB 18 (my real groups are actually bigger and so are my dataframe but you get the idea). I have looked at subset and aggregate but it doesn't work and the loop would be totally inefficient. I'm sure there is a function in R that does something like that but I couldn't find the proper keyword to search for it. Thanks for your help, Bastien __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Matrix- create mean/min/max/stdev on column of matrix or rows?
Hi: Here's a simple example that you can tune to your needs: m - matrix(rpois(100, 10), nrow = 10) # Function to compute summary statistics: f - function(x) c(min = min(x), med = median(x), mean = mean(x), max = max(x)) # Apply to rows (index 1) apply(m, 1, f) [,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9] [,10] min 5.0 7.0 5.0 6.0 5.0 5.0 8.0 5.0 2.0 6.0 med 11.5 9.5 10.0 9.5 9.0 8.0 10.0 10.0 6.0 10.0 mean 11.1 9.8 10.4 10.3 9.6 7.6 10.5 9.3 6.6 9.8 max 15.0 14.0 17.0 15.0 17.0 10.0 14.0 14.0 16.0 12.0 # Apply to columns (index 2) apply(m, 2, f) [,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9] [,10] min 3.0 6.0 5.0 6.0 2.0 5.0 5.0 5.0 8.0 6.0 med 9.0 9.5 11.0 9.5 8.5 9.5 9.0 6.0 10.5 10.0 mean 8.6 9.6 10.8 9.8 8.5 9.7 9.7 7.8 11.0 9.5 max 12.0 15.0 15.0 17.0 14.0 15.0 17.0 14.0 16.0 14.0 HTH, Dennis On Fri, Sep 17, 2010 at 9:08 AM, Halabi, Anan anan.hal...@hp.com wrote: I made simulation with Weibull and create Matrix, How can I create mean/min/max/stdev on column or rows of matrix?, Thanks, __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] convert to csv file
Hi: The first argument of ifelse is a logical statement that must evaluate to either TRUE or FALSE. I'm guessing that you're using the append function here, which is not a logical statement. Perhaps it would help if you described what you wanted to do with a reproducible example to illustrate the problem. HTH, Dennis On Fri, Sep 17, 2010 at 9:02 AM, lord12 gaut...@yahoo.com wrote: I get an error message: Error in file(file, ifelse(append, a, w)) : invalid 'open' argument How do I resolve this? -- View this message in context: http://r.789695.n4.nabble.com/convert-to-csv-file-tp2543232p2544070.html Sent from the R help mailing list archive at Nabble.com. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] convert to csv file
I might add that ifelse() is a vectorized function - is the operation you're trying to perform vectorized? D. On Fri, Sep 17, 2010 at 10:21 AM, Dennis Murphy djmu...@gmail.com wrote: Hi: The first argument of ifelse is a logical statement that must evaluate to either TRUE or FALSE. I'm guessing that you're using the append function here, which is not a logical statement. Perhaps it would help if you described what you wanted to do with a reproducible example to illustrate the problem. HTH, Dennis On Fri, Sep 17, 2010 at 9:02 AM, lord12 gaut...@yahoo.com wrote: I get an error message: Error in file(file, ifelse(append, a, w)) : invalid 'open' argument How do I resolve this? -- View this message in context: http://r.789695.n4.nabble.com/convert-to-csv-file-tp2543232p2544070.html Sent from the R help mailing list archive at Nabble.com. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] grouping dataframe entries using a categorical variable
Hi Bastien, You can use match(), or the convenience function %in%, like this (assuming your data.frame is named dat): subset(dat, ESS %in% c(EPB,SAB)) dat[dat$ESS %in% c(EPB,SAB), ] best, Ista On Fri, Sep 17, 2010 at 1:02 PM, Bastien Ferland-Raymond bastien.ferland-raymon...@ulaval.ca wrote: DearR Users, I have a problem which I think you might be able to help. I have a dataframe which I'm trying to filter following different groups I specified. It's a little hard to explain, so here is an example: My dataframe: ESS DHP 1 EPB 22 2 SAB 10 3 SAB 20 4 BOJ 14 5 ERS 28 11 SAB 10 12 SAB 22 13 BOJ 26 20 SAB 10 21 SAB 22 22 BOJ 32 29 SAB 14 30 SAB 22 38 SAB 14 47 SAB 18 I'm trying to filter it by selecting a subgroup of ESS, for example: softwood- c(EPB,SAB) So I can obtain: NEW dataframe: ESS DHP 1 EPB 22 2 SAB 10 3 SAB 20 11 SAB 10 12 SAB 22 20 SAB 10 21 SAB 22 29 SAB 14 30 SAB 22 38 SAB 14 47 SAB 18 (my real groups are actually bigger and so are my dataframe but you get the idea). I have looked at subset and aggregate but it doesn't work and the loop would be totally inefficient. I'm sure there is a function in R that does something like that but I couldn't find the proper keyword to search for it. Thanks for your help, Bastien __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. -- Ista Zahn Graduate student University of Rochester Department of Clinical and Social Psychology http://yourpsyche.org __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Combining Data Sets w/ Weights
On Sep 17, 2010, at 12:42 PM, btpagano wrote: Good News! I think I figured out my problem. The command I was looking for was append(). Er, maybe. It does appear that you could use append() but c() is much more the typical R way of concatenating objects like vectors and lists. The only advantage of append() over c() would appear to be the capacity for insertion of the second argument somewhere in the middle of the the first. The cbind and rbind functions are used for more complex objects like dataframes and matrices. -- David Winsemius, MD West Hartford, CT __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] grouping dataframe entries using a categorical variable
Bastien - In what way did subset(yourdataframe,ESS %in% softwood) not work? - Phil Spector Statistical Computing Facility Department of Statistics UC Berkeley spec...@stat.berkeley.edu On Fri, 17 Sep 2010, Bastien Ferland-Raymond wrote: DearR Users, I have a problem which I think you might be able to help. I have a dataframe which I'm trying to filter following different groups I specified. It's a little hard to explain, so here is an example: My dataframe: ESS DHP 1 EPB 22 2 SAB 10 3 SAB 20 4 BOJ 14 5 ERS 28 11 SAB 10 12 SAB 22 13 BOJ 26 20 SAB 10 21 SAB 22 22 BOJ 32 29 SAB 14 30 SAB 22 38 SAB 14 47 SAB 18 I'm trying to filter it by selecting a subgroup of ESS, for example: softwood- c(EPB,SAB) So I can obtain: NEW dataframe: ESS DHP 1 EPB 22 2 SAB 10 3 SAB 20 11 SAB 10 12 SAB 22 20 SAB 10 21 SAB 22 29 SAB 14 30 SAB 22 38 SAB 14 47 SAB 18 (my real groups are actually bigger and so are my dataframe but you get the idea). I have looked at subset and aggregate but it doesn't work and the loop would be totally inefficient. I'm sure there is a function in R that does something like that but I couldn't find the proper keyword to search for it. Thanks for your help, Bastien __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] Preparing data frame for Plotrix kiteChart
Although, I can fix this, I am trying to sort out something as straighforward as possible for my students, and I have some questions that hopefully someone can help me with. My data is: Species DistanceCount A 5 0 A 10 5 A 15 5 A 20 3 A 25 1 B 5 8 B 10 20 B 15 28 B 20 12 B 25 12 C 5 5 C 10 12 C 15 19 C 20 27 C 25 34 But I am struggling to get this into a data frame that does what I expect. I have tried various arrangements. What I am hoping for is: an x-axis labelled Distance with tick marks at 0, 5, 10,15,20 and 25. And, an y-axis labelled Species and tick marks labelled A, B and C. So I would appreciate some help on how the data should be prepared for kiteChart, to maximise the lablels being added automatically. If possible. Many thanks, Graham __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] keep par settings after device closes
On 16.09.2010 22:40, Jack Siegrist wrote: I am saving several plots to different formats. I want to be able to change the font size for all of them at once. Is there a way to do this without having to have a call to par every time a new device is opened? No. At least you will need some wrapper that does it for you. Uwe Ligges I know that the par settings are removed after each device is closed. Thanks for your help, Jack __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Nonlinear programming problem
Hi, You have not provided a reproducible example, so I can only make an educated guess. This is likely a numerical problem with trying to solve a linear system of equations in the Lagrange-Newton method (sequential quadratic programming or SQP) for solving nonlinearly programming problems. I am not sure what you can do about this, but here is a strategy: 1. be try a different, more reasonable, starting value. 2. If that does not help, you may want to check your problem specification to make sure that everything (objective function, constraints) is specified correctly 3. If (1) and (2) do not help, look at the scaling of the parameters, objective function, and the scaling of equality and inequality constraints. You can sometimes get convergence by simple scaling so that all these different entities are roughly of the same order of magnitude. 4. If all else fails, try a different algorithm. For example, the alabama package has `constrOptim.nl' function that you could try. But in future, when you ask these questions you should always send us a minimally self-contained, reproducible example, so that we can better help you. Hope this is helpful, Ravi. -Original Message- From: r-help-boun...@r-project.org [mailto:r-help-boun...@r-project.org] On Behalf Of Xiaoxi Gao Sent: Friday, September 17, 2010 2:03 AM To: R Help Subject: [R] Nonlinear programming problem Hello useRs, I'm using the command solnp in package Rsolnp to solve a general nonlinear programming problem. But I got an error that the leading minor of order 15 is not positive definite . Can anybody tell what may cause this error? Does it have something to do with the starting values? Thanks a lot!!! Xiaoxi [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Can I save my console contents automatically?
So it looks like the problem is with the mac GUI. Here are a couple more things to test. Try it with just sink and see if the output comes through. Also try with some other functions besides date (maybe summary(rnorm(100))). If there are other Mac users out there reading this, can some of you try as well and see if you get similar results? -- Gregory (Greg) L. Snow Ph.D. Statistical Data Center Intermountain Healthcare greg.s...@imail.org 801.408.8111 -Original Message- From: r-help-boun...@r-project.org [mailto:r-help-boun...@r- project.org] On Behalf Of Nobuaki Michihata Sent: Friday, September 17, 2010 7:03 AM To: r-help Subject: Re: [R] Can I save my console contents automatically? Hello Greg, Thank you for your comment. I had a chance to use Windows GUI R and I found several interesting differences between Mac and Windows GUI R. 1. txtStart() command - Windows GUI R - worked perfectly - Mac GUI R version.string R version 2.11.1 (2010-05-31) (both 32bit and 64bit) - only make a null file - Mac R version.string R version 2.11.1 (2010-05-31) on terminal window - worked perfectly (I also checked the permissions, but they were OK.) 2. Console - Mac GUI R can display very long results and can save them from the file menu (manually). - Windows GUI R can only short results and can save only the displayed results from the file menu. 3. sink() - Mac GUI R - split = TRUE worked. - Windows GUI R -split = TRUE didn't work (log on the file, but didn't display the results on the console). Thanks. Nobu Currently comments (#) are ignored by txtStart and friends due to the task callback mechanism used. The txtComment function is available as a work around to insert comments into the output/commands. I tried running date() as below and everything worked as expected (the comments were missing, but the date command and result were in the file. I am running on windows where it looks like you are running on unix or linux. Can you send your OS and version of R and TeachingDemos? Also what are the permissions on the logtest.txt file that is created? (I've seen problems where the permissions for a directory allowed the creating of a file, but the default permissions on the file then do not allow modification). -- Gregory (Greg) L. Snow Ph.D. Statistical Data Center Intermountain Healthcare greg.s...@imail.org 801.408.8111 -Original Message- From: r-help-boun...@r-project.org [mailto:r-help-boun...@r- project.org] On Behalf Of Nobuaki Michihata Sent: Thursday, September 16, 2010 8:24 AM To: r-help Subject: Re: [R] Can I save my console contents automatically? Hello David and Greg, Thank you for your suggestions. These really help me. I'm curious about txtStart function of TeachingDemos library. It looks exactly what I need. So I installed TeachingDemos library and tried following. - library(TeachingDemos) setwd(/Users/NOBU/Documents/R_data/) txtStart(logtest.txt, commands = TRUE, results = TRUE, append = FALSE) #Top of commands date() #End of commands txtStop() --- Then I got following outputs on my console window, but I only got a null file named logtest.txt. I tried several times by trial and error, but I couldn't find the solution to log outputs on the logtest.txt. --- library(TeachingDemos) setwd(/Users/NOBU/Documents/R_data/) txtStart(logtest.txt, commands = TRUE, results = TRUE, append = FALSE) Output being copied to text file, use txtStop to end txt txt #Top of commands txt date() [1] Thu Sep 16 07:16:29 2010 txt #End of commands txt txt txtStop() Thank you for your help! Nobu 2010/9/14 Nobuaki Michihata gha10...@gmail.com: Dear All, I found a following solution from http://r.789695.n4.nabble.com/;. However this command can save only the result. Is there any good solution to save both commands themselves and the results. Thank you for your help. sink(Filename_here.log, type=c(output,message), split=TRUE) # Put commands here # However this method save only the results. sink() Nobu Message: 33 Date: Fri, 10 Sep 2010 07:07:37 -0700 From: Nobuaki Michihata gha10...@gmail.com To: r-help@r-project.org, r-help@r-project.org Subject: [R] Can I save my console contents automatically? Message-ID: AANLkTimEZ-igqK6GzeYqERZaTg7m+chjbGJmAGmEL- y...@mail.gmail.com Content-Type: text/plain; charset=ISO-8859-1 Dear All, I'm using R for Mac OS X Cocoa GUI R version 2.11.1. I can save contents of my console window by using command + s, but I would like to do same thing using R commands. My question is can I save the contents automatically by using R editor with some R commands. Thank you. Nobu __ R-help@r-project.org mailing list
Re: [R] How to find STRESS criteria in MDS when there are negative eigenvalues....
Perhaps, the smacof package on CRAN might be useful to you.
Ravi.
-Original Message-
From: r-help-boun...@r-project.org [mailto:r-help-boun...@r-project.org] On
Behalf Of Na.Ebrahimi
Sent: Friday, September 17, 2010 11:08 AM
To: r-help@r-project.org
Subject: [R] How to find STRESS criteria in MDS when there are negative
eigenvalues
Hi,
I want to know whether there is any function in R to find STRESS after using
cmdscale and estimating the coordinates, I have written these functions to
find stress (for p =1,2,3,4,5)
stress-rep(0,5)
for(p in 1:5)
{
datahat-cmdscale(d,p)
deltahat-as.matrix(dist(datahat))
a-0
b-0
for(i in 1:n)
{
for(j in 1:n)
{
a-d[i,j]^2+a
b-(d[i,j]-deltahat[i,j])^2+b
}
}
stress[p]-b/a
}
stress-sqrt(stress)
stress
but it seems that it is not true when there are negative eigenvalues in
dissimilarity matrix could you please help me to find the answer
thank you in anticipation
[[alternative HTML version deleted]]
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__
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PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
Re: [R] Preparing data frame for Plotrix kiteChart
Graham Smith graham.smith at myotis.co.uk writes: Although, I can fix this, I am trying to sort out something as straighforward as possible for my students, and I have some questions that hopefully someone can help me with. My data is: Species DistanceCount A 5 0 A 10 5 A 15 5 A 20 3 A 25 1 B 5 8 B 10 20 B 15 28 B 20 12 B 25 12 C 5 5 C 10 12 C 15 19 C 20 27 C 25 34 But I am struggling to get this into a data frame that does what I expect. I have tried various arrangements. What I am hoping for is: an x-axis labelled Distance with tick marks at 0, 5, 10,15,20 and 25. And, an y-axis labelled Species and tick marks labelled A, B and C. So I would appreciate some help on how the data should be prepared for kiteChart, to maximise the lablels being added automatically. If possible. Many thanks, Graham X - read.table(textConnection(Species DistanceCount A 5 0 A 10 5 A 15 5 A 20 3 A 25 1 B 5 8 B 10 20 B 15 28 B 20 12 B 25 12 C 5 5 C 10 12 C 15 19 C 20 27 C 25 34),header=TRUE) library(reshape) X2 - recast(X,Distance~Species,id.var=1:2) X3 - as.matrix(X2[,-1]) rownames(X3) - X2$Distance colnames(X3) - names(X2)[-1] library(plotrix) kiteChart(t(X3),xlab=Distance,ylab=Species) __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Can I save my console contents automatically?
On Sep 17, 2010, at 2:04 PM, Greg Snow wrote: So it looks like the problem is with the mac GUI. Here are a couple more things to test. Try it with just sink and see if the output comes through. Also try with some other functions besides date (maybe summary(rnorm(100))). If there are other Mac users out there reading this, can some of you try as well and see if you get similar results? Greg; Running the example on your txtStart help page did not seem to produce any file output that the Finder.app interface recognized as being created on this date. However that app does not do a full systemwide search. Then ... running the system() calls to enscript and ps2pdf did produce evidence that somewhere an external log existed, since I got ps and pdf files with the message and histogram (but no console input). R version 2.11.1 Patched (2010-06-14 r52281) [R.app GUI 1.35 (5590) x86_64-apple-darwin9.8.0] MacOSX 10.5.8 -- David. -- Gregory (Greg) L. Snow Ph.D. Statistical Data Center Intermountain Healthcare greg.s...@imail.org 801.408.8111 -Original Message- From: r-help-boun...@r-project.org [mailto:r-help-boun...@r- project.org] On Behalf Of Nobuaki Michihata Sent: Friday, September 17, 2010 7:03 AM To: r-help Subject: Re: [R] Can I save my console contents automatically? Hello Greg, Thank you for your comment. I had a chance to use Windows GUI R and I found several interesting differences between Mac and Windows GUI R. 1. txtStart() command - Windows GUI R - worked perfectly - Mac GUI R version.string R version 2.11.1 (2010-05-31) (both 32bit and 64bit) - only make a null file - Mac R version.string R version 2.11.1 (2010-05-31) on terminal window - worked perfectly (I also checked the permissions, but they were OK.) 2. Console - Mac GUI R can display very long results and can save them from the file menu (manually). - Windows GUI R can only short results and can save only the displayed results from the file menu. 3. sink() - Mac GUI R - split = TRUE worked. - Windows GUI R -split = TRUE didn't work (log on the file, but didn't display the results on the console). Thanks. Nobu Currently comments (#) are ignored by txtStart and friends due to the task callback mechanism used. The txtComment function is available as a work around to insert comments into the output/commands. I tried running date() as below and everything worked as expected (the comments were missing, but the date command and result were in the file. I am running on windows where it looks like you are running on unix or linux. Can you send your OS and version of R and TeachingDemos? Also what are the permissions on the logtest.txt file that is created? (I've seen problems where the permissions for a directory allowed the creating of a file, but the default permissions on the file then do not allow modification). -- Gregory (Greg) L. Snow Ph.D. Statistical Data Center Intermountain Healthcare greg.s...@imail.org 801.408.8111 -Original Message- From: r-help-boun...@r-project.org [mailto:r-help-boun...@r- project.org] On Behalf Of Nobuaki Michihata Sent: Thursday, September 16, 2010 8:24 AM To: r-help Subject: Re: [R] Can I save my console contents automatically? Hello David and Greg, Thank you for your suggestions. These really help me. I'm curious about txtStart function of TeachingDemos library. It looks exactly what I need. So I installed TeachingDemos library and tried following. - library(TeachingDemos) setwd(/Users/NOBU/Documents/R_data/) txtStart(logtest.txt, commands = TRUE, results = TRUE, append = FALSE) #Top of commands date() #End of commands txtStop() --- Then I got following outputs on my console window, but I only got a null file named logtest.txt. I tried several times by trial and error, but I couldn't find the solution to log outputs on the logtest.txt. --- library(TeachingDemos) setwd(/Users/NOBU/Documents/R_data/) txtStart(logtest.txt, commands = TRUE, results = TRUE, append = FALSE) Output being copied to text file, use txtStop to end txt txt #Top of commands txt date() [1] Thu Sep 16 07:16:29 2010 txt #End of commands txt txt txtStop() Thank you for your help! Nobu 2010/9/14 Nobuaki Michihata gha10...@gmail.com: Dear All, I found a following solution from http://r.789695.n4.nabble.com/;. However this command can save only the result. Is there any good solution to save both commands themselves and the results. Thank you for your help. sink(Filename_here.log, type=c(output,message), split=TRUE) # Put commands here # However this method save only the results. sink() Nobu Message: 33 Date: Fri, 10 Sep 2010 07:07:37 -0700 From: Nobuaki Michihata gha10...@gmail.com To: r-help@r-project.org, r-help@r-project.org Subject: [R] Can I save my console contents automatically? Message-ID: AANLkTimEZ-igqK6GzeYqERZaTg7m+chjbGJmAGmEL- y...@mail.gmail.com Content-Type: text/plain; charset=ISO-8859-1 Dear All, I'm
Re: [R] Is there a project to compile R scripts into stand-alone executable file?
yehengxin xye78 at hotmail.com writes: I know Matlab's M file can be converted to a stand-alone executable file. I wonder if there is a project aimed at compiling R scripts into stand-alone executable file. I think it will be very promising for R to be more widely used in different fields. You could ask in R-devel, but so far there has been no one who has needed this badly enough to go to the trouble of doing it. What is your use case? __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] troubles with R
Dear friends, thank you Liina Pilv On Jan 24, 2010, at 6:56 PM, Jim Holtman wrote: where did you save it to; what directory? did you restart in the same directory? most likely a procedural error. What is the problem you are trying to solve? Sent from my iPhone. On Jan 24, 2010, at 9:46, Liina Pilv li...@kodu.ee wrote: Dear adviser, I am fond of R, and enjoy it very much. But... I have great problems. I have saved the data before quitting but when I return to the R session I can not find my saved Data again. It is said: Data which is saved will be available in future R sessions. ... is not TRUE. I work with iMAC (System Version:Mac OS X 10.5.8 (9L31a); Kernel Version: Darwin 9.8.0) There should be some differences between UNIX and Mac. thankfully waiting your answer Liina Pilv GP in Estonia [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] lmer() vs. lme() gave different variance component estimates
Hi, I asked this on mixed model mailing list, but that list is not very active, so I'd like to try the general R mailing list. Sorry if anyone receives the double post. Hi, I have a dataset of animals receiving some eye treatments. There are 8 treatments, each animal's right and left eye was measured with some scores (ranging from 0 to 7) 4 times after treatment. So there are nesting groups eyes within animal. Dataset attached dat-read.table(dat.txt,sep='\t',header=T,row.names=1) dat$id-factor(dat$id) str(dat) 'data.frame': 640 obs. of 5 variables: $ score: int 0 2 0 7 4 7 0 2 0 7 ... $ id : Factor w/ 80 levels 1,3,6,10,..: 7 48 66 54 18 26 38 52 39 63 ... $ rep : int 1 1 1 1 1 1 1 1 1 1 ... $ eye : Factor w/ 2 levels L,R: 2 2 2 2 2 2 2 2 2 2 ... $ trt : Factor w/ 8 levels A,B,C,Control,..: 1 1 1 1 1 1 1 1 1 1 ... I fit a mixed model using both lmer() from lme4 package and lme() from nlme package: lmer(score~trt+(1|id/eye),dat) Linear mixed model fit by REML Formula: score ~ trt + (1 | id/eye) Data: dat AIC BIC logLik deviance REMLdev 446.7 495.8 -212.4430.9 424.7 Random effects: Groups NameVariance Std.Dev. eye:id (Intercept) 6.9208e+00 2.630742315798 id (Intercept) 1.4471e-16 0.00012030 Residual 1.8750e-02 0.136930641909 Number of obs: 640, groups: eye:id, 160; id, 80 summary(lme(score~trt, random=(~1|id/eye), dat)) Linear mixed-effects model fit by REML Data: dat AIC BIClogLik 425.1569 474.0947 -201.5785 Random effects: Formula: ~1 | id (Intercept) StdDev:1.873576 Formula: ~1 | eye %in% id (Intercept) Residual StdDev:1.896126 0.1369306 As you can see, the variance components estimates of random effects are quite different between the 2 model fits. From the data, I know that the variance component for id can't be near 0, which is what lmer() fit produced, so I think the lme() fit is correct while lmer() fit is off. This can also be seen from AIC, BIC etc. lme() fit has better values than lmer() fit. I guess this might be due to lmer() didn't converge very well, is there anyway to adjust to make lmer() converge better to get similar results as lme()? Thanks John score id rep eye trt 1 0 15 1 R A 2 2 72 1 R A 3 0 102 1 R A 4 7 82 1 R A 5 4 28 1 R A 6 7 42 1 R A 7 0 60 1 R A 8 2 79 1 R A 9 0 61 1 R A 10 7 95 1 R A 11 0 15 2 R A 12 2 72 2 R A 13 0 102 2 R A 14 7 82 2 R A 15 4 28 2 R A 16 7 42 2 R A 17 0 60 2 R A 18 2 79 2 R A 19 0 61 2 R A 20 7 95 2 R A 21 0 15 3 R A 22 2 72 3 R A 23 0 102 3 R A 24 7 82 3 R A 25 4 28 3 R A 26 7 42 3 R A 27 0 60 3 R A 28 2 79 3 R A 29 0 61 3 R A 30 7 95 3 R A 31 0 15 4 R A 32 2 72 4 R A 33 0 102 4 R A 34 7 82 4 R A 35 4 28 4 R A 36 7 42 4 R A 37 0 60 4 R A 38 2 79 4 R A 39 0 61 4 R A 40 7 95 4 R A 41 3 15 1 L A 42 0 72 1 L A 43 0 102 1 L A 44 5 82 1 L A 45 0 28 1 L A 46 7 42 1 L A 47 0 60 1 L A 48 0 79 1 L A 49 0 61 1 L A 50 7 95 1 L A 51 3 15 2 L A 52 0 72 2 L A 53 0 102 2 L A 54 5 82 2 L A 55 0 28 2 L A 56 7 42 2 L A 57 0 60 2 L A 58 0 79 2 L A 59 0 61 2 L A 60 7 95 2 L A 61 3 15 3 L A 62 0 72 3 L A 63 0 102 3 L A 64 5 82 3 L A 65 0 28
[R] how to work with Year-Month dates
Hi all, Is there a built in or easier way to work with dates that are *just* Year-Month? Right now I paste() on a day as a work around, but it ultimately needs to be in Year-Month form, so then I use format() to get rid of the day. x - c(2006-December, 2006-July) x - paste(x, -01, sep='') x - as.Date(x, %Y-%B-%d) x - sort(x) x - format(x, format = %Y-%B) x [1] 2006-July 2006-December Thanks, Josh -- Joshua Wiley Ph.D. Student, Health Psychology University of California, Los Angeles http://www.joshuawiley.com/ __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] how to work with Year-Month dates
Try this: library(zoo) as.yearmon(x, %Y-%B) On Fri, Sep 17, 2010 at 4:23 PM, Joshua Wiley jwiley.ps...@gmail.comwrote: Hi all, Is there a built in or easier way to work with dates that are *just* Year-Month? Right now I paste() on a day as a work around, but it ultimately needs to be in Year-Month form, so then I use format() to get rid of the day. x - c(2006-December, 2006-July) x - paste(x, -01, sep='') x - as.Date(x, %Y-%B-%d) x - sort(x) x - format(x, format = %Y-%B) x [1] 2006-July 2006-December Thanks, Josh -- Joshua Wiley Ph.D. Student, Health Psychology University of California, Los Angeles http://www.joshuawiley.com/ __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. -- Henrique Dallazuanna Curitiba-Paraná-Brasil 25° 25' 40 S 49° 16' 22 O [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] odfWeave UTF-8 error and latin characters
Hello R masters,
I have sent this same message to other lists and none so far could give some
light. I was trying to use odfWeave to generate a report from R and Im
getting an error that I think is related to latin characters. I looked
around and did find some stuff related to this problem about Sweave
http://labmoluscos.wordpress.com/2010/02/18/sweave-latex-character-encoding/
but
did not find a way to fix it so far for odfWeave. Perhaps some one could
give me some light on how to workaround it.
I think my problem is that I have a table with characters such as 'ç', 'ó'
and 'ã' that odfWeave is not recognizing properly. The error follows below.
Just to make it clear: Windows vista (default language - Brazilian
Portuguese), R 2.11.1, odfWeave 0.7.11, OpenOffice 3.0.1
in my odt file ...
tabela2, echo = FALSE, results = xml=
odfTable(tabela2,useRowNames=T,name ='Tabela 2')
@
in R console ...
library(odfWeave)
imageDefs - getImageDefs()
imageDefs$type - 'bmp'
imageDefs$device - 'bmp'
setImageDefs(imageDefs)
options(SweaveSyntax=SweaveSyntaxNoweb)
odfWeave('teste.odt','figura1.odt')
Copying teste.odt
Setting wd to
C:\Users\PEDROE~1\AppData\Local\Temp\Rtmpfv32oJ/odfWeave0215405313
Unzipping ODF file using unzip -o teste.odt
Archive: teste.odt
extracting: mimetype
creating: Configurations2/statusbar/
inflating: Configurations2/accelerator/current.xml
creating: Configurations2/floater/
creating: Configurations2/popupmenu/
creating: Configurations2/progressbar/
creating: Configurations2/menubar/
creating: Configurations2/toolbar/
creating: Configurations2/images/Bitmaps/
inflating: content.xml
inflating: styles.xml
extracting: meta.xml
inflating: Thumbnails/thumbnail.png
inflating: settings.xml
inflating: META-INF/manifest.xml
Removing teste.odt
Creating a Pictures directory
Pre-processing the contents
Sweaving content.Rnw
Writing to file content_1.xml
Processing code chunks ...
1 : term verbatim(label=fluxograma)
Loading required package: shape
Loading required package: shape
2 : term xml(label=tabela2)
'content_1.xml' has been Sweaved
Removing content.xml
Post-processing the contents
Input is not proper UTF-8, indicate encoding !
Bytes: 0xE2 0x6E 0x63 0x69
Erro: 1: Input is not proper UTF-8, indicate encoding !
Bytes: 0xE2 0x6E 0x63 0x69
tabela2[1:5,] # a piece of table 2
Concordância observada Kappa p valor
Sexo: 1. 1. 0e+00
Referenciamento para diagnóstico: 0.6863 0.5081 4e-03
Reteste na doação de sangue:0.9379 0.7874 0e+00
Resultado do reteste da doação: 0.9317 0.6607 2e-04
Indicação médica para investigação: 0.6957 0.5556 1e-04
Considering some sugestions form other lists I tryed to encode the table
using enc2utf8 and descr::toUTF8 such as
tabela2, echo = FALSE, results = xml=
odfTable(enc2utf8(tabela2),useRowNames=T,name ='Tabela 2')
@
OR
tabela2, echo = FALSE, results = xml=
enc2utf8(odfTable(tabela2,useRowNames=T,name ='Tabela 2'))
@
OR
tabela2, echo = FALSE, results = xml=
toUTF8(odfTable(tabela2,useRowNames=T,name ='Tabela 2'))
@
But all of them gave the same error. However, if I set the table without the
rownames such as:
tabela2, echo = FALSE, results = xml=
odfTable(tabela2,useRowNames=F,name ='Tabela 2')
@
It works fine... but the rownames are not there. I tryed to bind the
rownames as column but the error comes back.
After a couple days banging my head around Im about to appeal to old friend
copy and paste. Any sugestion is most welcome.
Kind regards to all and thanks in advance,
Abraço forte e que a força esteja com você,
Dr. Pedro Emmanuel A. A. do Brasil
Instituto de Pesquisa Clínica Evandro Chagas
Fundação Oswaldo Cruz
Rio de Janeiro - Brasil
Av. Brasil 4365
Tel 55 21 3865-9648
email: pedro.bra...@ipec.fiocruz.br
email: emmanuel.bra...@gmail.com
---Apoio aos softwares livres
www.zotero.org - gerenciamento de referências bibliográficas.
www.broffice.org ou www.openoffice.org - textos, planilhas ou apresentações.
www.epidata.dk - entrada de dados.
www.r-project.org - análise de dados.
www.ubuntu.com - sistema operacional
[[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.
Re: [R] Is there a bisection method in R?
If uniroot is not a bisection method, then what function in R does use bisection? Thanks. --- On Fri, 9/10/10, David Winsemius dwinsem...@comcast.net wrote: From: David Winsemius dwinsem...@comcast.net Subject: Re: [R] Is there a bisection method in R? To: huang min minhua...@gmail.com Cc: Gregory Gentlemen gregory_gentle...@yahoo.ca, r-help@r-project.org Received: Friday, September 10, 2010, 9:56 PM On Sep 10, 2010, at 8:35 PM, huang min wrote: uniroot ... is not a bisection method. On Sat, Sep 11, 2010 at 6:10 AM, Gregory Gentlemen gregory_gentle...@yahoo.ca wrote: Dear fellow R-users, Is there a function that does the bisection method? I was unable to find one. Thanks in advance. Gregory --David Winsemius, MD West Hartford, CT [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] how to work with Year-Month dates
I had started thinking of writing my own class...this is much nicer. Thanks! Josh On Fri, Sep 17, 2010 at 12:27 PM, Henrique Dallazuanna www...@gmail.com wrote: Try this: library(zoo) as.yearmon(x, %Y-%B) On Fri, Sep 17, 2010 at 4:23 PM, Joshua Wiley jwiley.ps...@gmail.com wrote: Hi all, Is there a built in or easier way to work with dates that are *just* Year-Month? Right now I paste() on a day as a work around, but it ultimately needs to be in Year-Month form, so then I use format() to get rid of the day. x - c(2006-December, 2006-July) x - paste(x, -01, sep='') x - as.Date(x, %Y-%B-%d) x - sort(x) x - format(x, format = %Y-%B) x [1] 2006-July 2006-December Thanks, Josh -- Joshua Wiley Ph.D. Student, Health Psychology University of California, Los Angeles http://www.joshuawiley.com/ __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. -- Henrique Dallazuanna Curitiba-Paraná-Brasil 25° 25' 40 S 49° 16' 22 O -- Joshua Wiley Ph.D. Student, Health Psychology University of California, Los Angeles http://www.joshuawiley.com/ __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] function help?
On 9/17/10 12:46 PM, Jeff Newmiller wrote: If having the definition of the function appear when you enter the name of the function elicits a hate response, then perhaps you should not be using R. That characteristic of R is fundamental and unlikely to change: in R everything is an object, and the result of evaluating an expression is displayed at the command line. Other languages have different unifying principles, and may be appropriate for different tasks. Well, *hate* or *love* is just a matter of time and / or habit, so it will not interfere with me doing anything, especially in work related. I dont mind learning anything that will serve me well. Indeed, some projects that I am currently working with involve some R packages and hence some R coding as well, so I will use R no matter if I hate it or not. Anything that can be done in R could be done in, say, C, but by the time you did so you might find yourself learning very similar lessons to the ones R assumes you know. I have zero background on programming, so I prefer to work and learn in C/C++ if I have a chance (and time). But if I need something quick, then I will have to use something like matlab, R or python. Dukeduke.li...@gmx.com wrote: On 9/16/10 5:00 PM, Rolf Turner wrote: On 17/09/2010, at 8:51 AM, Duke wrote: Hi Duncan, On 9/16/10 3:47 PM, Duncan Murdoch wrote: On 16/09/2010 3:40 PM, Duke wrote: Hi all, I am writing a function (fun.R), but I dont know how to code the function so that the Help Text will be shown up when one types ?fun (of course, after he loads it up). Anyone has any advice for me how to do that? The help text is separate from the function (unless you use the roxygen package or similar). You need to write a package so that R will find the help; instructions are in the Writing R Extensions manual. I was expecting something simpler than writing a package, and that I can integrate it into fun.R, but thanks anyway. (a) Writing a package is not all that hard. You can say so if you are fluent in R. I just started and have written only 20-30 lines of codes so far. Also, writing a package is still more complicated than writing a simple function (single file). Why R is so different from other languages (python, matlab or more basics like C/C++ etc...)? In fact I still feel very uncomfortable with R, for example, I hate when I type a function name, it shows the whole function. Honestly I feel a world of programming is a mess, and it is tough when one wants to jump from one language to another. (b) It focuses the mind wondrously. I did try to write a simple package (followed a tutorial), but did not find what you said :). Maybe I need more practice. (c) Using R CMD check on the package is very useful for picking the lint off the code. It would be great if you share your experience a little more about this. Thanks, D. cheers, Rolf Turner ## Attention: This e-mail message is privileged and confidential. If you are not the intended recipient please delete the message and notify the sender. Any views or opinions presented are solely those of the author. This e-mail has been scanned and cleared by MailMarshal www.marshalsoftware.com ## __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. --- Jeff NewmillerThe . . Go Live... DCN:jdnew...@dcn.davis.ca.us Basics: ##.#. ##.#. Live Go... Live: OO#.. Dead: OO#.. Playing Research Engineer (Solar/BatteriesO.O#. #.O#. with /Software/Embedded Controllers) .OO#. .OO#. rocks...1k --- Sent from my phone. Please excuse my brevity. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] lmer() vs. lme() gave different variance component estimates
On 09/17/2010 09:14 PM, array chip wrote: Hi, I asked this on mixed model mailing list, but that list is not very active, so I'd like to try the general R mailing list. Sorry if anyone receives the double post. Hi, I have a dataset of animals receiving some eye treatments. There are 8 treatments, each animal's right and left eye was measured with some scores (ranging from 0 to 7) 4 times after treatment. So there are nesting groups eyes within animal. Dataset attached dat-read.table(dat.txt,sep='\t',header=T,row.names=1) dat$id-factor(dat$id) str(dat) 'data.frame': 640 obs. of 5 variables: $ score: int 0 2 0 7 4 7 0 2 0 7 ... $ id : Factor w/ 80 levels 1,3,6,10,..: 7 48 66 54 18 26 38 52 39 63 ... $ rep : int 1 1 1 1 1 1 1 1 1 1 ... $ eye : Factor w/ 2 levels L,R: 2 2 2 2 2 2 2 2 2 2 ... $ trt : Factor w/ 8 levels A,B,C,Control,..: 1 1 1 1 1 1 1 1 1 1 ... I fit a mixed model using both lmer() from lme4 package and lme() from nlme package: lmer(score~trt+(1|id/eye),dat) Linear mixed model fit by REML Formula: score ~ trt + (1 | id/eye) Data: dat AIC BIC logLik deviance REMLdev 446.7 495.8 -212.4430.9 424.7 Random effects: Groups NameVariance Std.Dev. eye:id (Intercept) 6.9208e+00 2.630742315798 id (Intercept) 1.4471e-16 0.00012030 Residual 1.8750e-02 0.136930641909 Number of obs: 640, groups: eye:id, 160; id, 80 summary(lme(score~trt, random=(~1|id/eye), dat)) Linear mixed-effects model fit by REML Data: dat AIC BIClogLik 425.1569 474.0947 -201.5785 Random effects: Formula: ~1 | id (Intercept) StdDev:1.873576 Formula: ~1 | eye %in% id (Intercept) Residual StdDev:1.896126 0.1369306 As you can see, the variance components estimates of random effects are quite different between the 2 model fits. From the data, I know that the variance component for id can't be near 0, which is what lmer() fit produced, so I think the lme() fit is correct while lmer() fit is off. This can also be seen from AIC, BIC etc. lme() fit has better values than lmer() fit. I guess this might be due to lmer() didn't converge very well, is there anyway to adjust to make lmer() converge better to get similar results as lme()? That's your guess... I'd be more careful about jumping to conclusions. If this is a balanced data set, perhaps you could supply the result of summary(aov(score~trt+Error(id/eye), data=dat)) The correct estimates should be computable from the ANOVA table. -- Peter Dalgaard Center for Statistics, Copenhagen Business School Phone: (+45)38153501 Email: pd@cbs.dk Priv: pda...@gmail.com __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Is there a bisection method in R?
Why does it matter what method is used? The uniroot function used a quicker method than bisection, but solves the same problem, so why do you need bisection? The only reason I can think is this is a homework problem, in which case we don't do homework. In fact I have assigned this as homework before (to write a function to find roots using bisection) so I know it has been done, and is not that hard for you to do yourself. -- Gregory (Greg) L. Snow Ph.D. Statistical Data Center Intermountain Healthcare greg.s...@imail.org 801.408.8111 -Original Message- From: r-help-boun...@r-project.org [mailto:r-help-boun...@r- project.org] On Behalf Of Gregory Gentlemen Sent: Friday, September 17, 2010 1:29 PM To: huang min; David Winsemius Cc: r-help@r-project.org Subject: Re: [R] Is there a bisection method in R? If uniroot is not a bisection method, then what function in R does use bisection? Thanks. --- On Fri, 9/10/10, David Winsemius dwinsem...@comcast.net wrote: From: David Winsemius dwinsem...@comcast.net Subject: Re: [R] Is there a bisection method in R? To: huang min minhua...@gmail.com Cc: Gregory Gentlemen gregory_gentle...@yahoo.ca, r-h...@r- project.org Received: Friday, September 10, 2010, 9:56 PM On Sep 10, 2010, at 8:35 PM, huang min wrote: uniroot ... is not a bisection method. On Sat, Sep 11, 2010 at 6:10 AM, Gregory Gentlemen gregory_gentle...@yahoo.ca wrote: Dear fellow R-users, Is there a function that does the bisection method? I was unable to find one. Thanks in advance. Gregory --David Winsemius, MD West Hartford, CT [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting- guide.html and provide commented, minimal, self-contained, reproducible code. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Is there a bisection method in R?
On 09/17/2010 09:28 PM, Gregory Gentlemen wrote: If uniroot is not a bisection method, then what function in R does use bisection? Why do you assume that there is one? uniroot contains a better algorithm for finding bracketed roots. It shouldn't be too hard to roll your own if you need one for pedagogical purposes. -- Peter Dalgaard Center for Statistics, Copenhagen Business School Phone: (+45)38153501 Email: pd@cbs.dk Priv: pda...@gmail.com __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] glm: formula vs character
I think what is going on (and someone is likely to correct me otherwise) is
that formulas have an associated environment that gets passed along with them
while character strings do not.
This means that when you pass the object to another function which passes it to
another function, etc. that eventually one of those nested functions is going
to do something with the formula, if it is an actual formula then it can look
in that environment that has been passed along and find the variables that the
formula refers to and everything is happy.
When you just use the text string, the deeply nested function that is using it
does not know where to look for the variables referred to in the formula and
you get your error.
Hope this helps,
--
Gregory (Greg) L. Snow Ph.D.
Statistical Data Center
Intermountain Healthcare
greg.s...@imail.org
801.408.8111
-Original Message-
From: r-help-boun...@r-project.org [mailto:r-help-boun...@r-
project.org] On Behalf Of Krishna Tateneni
Sent: Thursday, September 16, 2010 4:56 PM
To: r-help
Subject: [R] glm: formula vs character
Hello,
This is a question motivated by curiosity, not a pressing problem. Any
responses are much appreciated! In the following code, function reg1
calls
glm with a formula object while reg2 uses a string. In both cases, glm
works; however, in the second case, the add1 function fails with the
following message: Error in eval(predvars, data, env) : invalid
'envir'
argument. Any insight into what is going on under the hood?
Many thanks,
--Krishna
x1 = rnorm(100)
x2 = rnorm(100)
x3 = rnorm(100)
y = x1 + 2*x2 + 3*x3 + 0.05*rnorm(100)
d = data.frame(y,x1,x2,x3)
xset = paste(x,1:3,sep=)
reg1-function(dep,cand,data){
f = paste(dep,~1,sep=)
reg = glm(as.formula(f),family=gaussian,data)
add = add1(reg,cand,test=F)
}
reg2-function(dep,cand,data){
f = paste(dep,~1,sep=)
reg = glm(f,family=gaussian,data)
add = add1(reg,cand,test=F)
}
r1 = reg1(y,xset,d)
r2 = reg2(y,xset,d)
[[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.
__
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PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
Re: [R] Help with graphic margin
I can't see the graphs (my work has a rather strict policy about file sharing websites and apparently imageshack is redlisted). But try adding outer=TRUE to the axis function calls and see if that fixes the problem. If not, play with the par(xpd= ) setting. -- Gregory (Greg) L. Snow Ph.D. Statistical Data Center Intermountain Healthcare greg.s...@imail.org 801.408.8111 -Original Message- From: r-help-boun...@r-project.org [mailto:r-help-boun...@r- project.org] On Behalf Of Filoche Sent: Thursday, September 16, 2010 5:55 PM To: r-help@r-project.org Subject: Re: [R] Help with graphic margin Hi there and thank you for reply. I have been trying that, using mar to set margin around each plot and oma to specify bottom space. However, it wont display the xlab. Here's my code : pdf(file=/home/persican/Desktop/test.pdf, width = 3.5, height = 5.6, pointsize = 8); par(mfcol = c(3,1), mar = c(1,1,1,1), oma = c(10,1,1,1)); plot(x,y, pch = 21, bg = gray, xaxt = n, yaxt = n, ylab = ylab); ... plot(x,y, pch = 21, bg = gray, xaxt = n, yaxt = n, ylab = ylab); ... plot(x,y, pch = 21, bg = gray, xaxt = n, yaxt = n, ylab = ylab, xlab =X axis); axis(1, tck = 0.02); axis(2, tck = 0.02); dev.off(); This produce : http://img837.imageshack.us/img837/5397/testpdfpages.jpg http://img837.imageshack.us/img837/5397/testpdfpages.jpg As we can figure, we dont see the xlab on the last plot. With regards, Phil -- View this message in context: http://r.789695.n4.nabble.com/Help-with- graphic-margin-tp2542469p2543136.html Sent from the R help mailing list archive at Nabble.com. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting- guide.html and provide commented, minimal, self-contained, reproducible code. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] Data Cube in R from CSV
Hello I am at the moment trying to get to grips with a data cube in R, and I am increasingly wondering whether I am actually making things unnecessarily difficult for myself. The idea is that I have a data cube with three dimensions (so a 3D matrix): companies, figures, and years. So along the z axis the vectors are essentially time series, the horizontals are all about a single figure and the verticals are all the data from a single company. I create the data cube with the reshape package from a 2D CSV file (which in turn is saved as a CSV file from an Excel File, which is the data master), which works so far very fine indeed. Data_m-melt(Data, id=1:8, na.rm=TRUE) Data_cube-cast(Data_m, Figure~Company~variable) The question now comes how one can browse through this object, as view gives it out as A.B and gets rather large. Does anyone know a way to save resulting data cubes elegantly, i.e. maybe so that there is a tool where one can scroll through the result, etc. ? I presume there are several researchers here who also find that Excel is not at all levels the best repository for R data, but who don't want to toy around with Linux and for whom Matlab + Stats box is a little pricey. -- View this message in context: http://r.789695.n4.nabble.com/Data-Cube-in-R-from-CSV-tp2544404p2544404.html Sent from the R help mailing list archive at Nabble.com. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Preparing data frame for Plotrix kiteChart
Ben, Thanks for your help on this. Obviously a bit of a mental block on my part, as it seems painfully obvious now. Graham __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] Merging data frames on a variety of columns
Hello, This is a semi-complicated question about comparing two datasets, probably using merge, but I am open to other ideas. I have a large frame of information about companies. It's over 30,000 rows and looks something like... df1 - identifier1 identifier2nameother_nameyear H34 C56 ACME ACME_LTD 2001 H34 NAACME ACME_LTD 2002 X20 C40 FOO_COFOO_CO 2004 NANABAR_SABAR_SAB2004 NANABAR_SABAR_SAB2005 As you can see, many observations are missing values. I have a second data frame with information about these same companies, in fewer rows, and often with slightly different info... df2 - identifier1 identifier2name year H34 NAACME_LTD 2001 H34 NAACME_LTD 2002 X20 C40 FOO2004 The idea is to figure out which companies in the first set are not in the second set. My approach so far is to do various merges and then remove the matches from the original data frame... m1 - merge(df1, df2, by = c(identifier1, identifier2, year), incomparables=NA) m2 - merge(df1, df2, by = c(name, year), incomparables=NA) m3 - merge(df1, df2, by.x = c(other_name, year), by.y = c(name, year), incomparables = NA) Is this really the best way to accomplish my goal? Also, for some reason when I do merges like m3, my resulting data frame is missing columns and I am getting rows that do not appear to match on the variables I have specified, e.g. ... year other_name identifier1name identifier2 2001 AMDOCS_LTDG0260210 AMDOCS_LTDED C42913 Help is much appreciated, Chris __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] lmer() vs. lme() gave different variance component estimates
Thank you Peter. Actually 3 people from mixed model mailing list tried my code using lmer(). They got the same results as what I got from lme4(). So they couldn't replicate my lmer() results: Random effects: Groups NameVariance Std.Dev. eye:id (Intercept) 3.59531 1.89613 id (Intercept) 3.51025 1.87357 Residual 0.01875 0.13693 Number of obs: 640, groups: eye:id, 160; id, 80 The only difference they can think of is they are using Mac and FreeBSD while mine is PC. I can't imagine this can be the reason. I re-install lme4 package, but still got weird results with lmer(). Per your suggestion, here is the results for aov() summary(aov(score~trt+Error(id/eye), data=dat)) Error: id Df Sum Sq Mean Sq F valuePr(F) trt7 1353.6 193.378 4.552 0.0002991 *** Residuals 72 3058.7 42.482 --- Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1 Error: id:eye Df Sum Sq Mean Sq F value Pr(F) Residuals 80 115214.4 Error: Within Df Sum Sq Mean Sq F value Pr(F) Residuals 480 9 0.01875 As can be seen, thr within subject variance estimate (0.01875) is the same between aov, lmer and lme. But I am not sure how to relate results between aov and lmer/lme for the other 2 variance components (id and eye%in%id). Thanks John - Original Message From: Peter Dalgaard pda...@gmail.com To: array chip arrayprof...@yahoo.com Cc: r-help@r-project.org Sent: Fri, September 17, 2010 1:05:27 PM Subject: Re: [R] lmer() vs. lme() gave different variance component estimates On 09/17/2010 09:14 PM, array chip wrote: Hi, I asked this on mixed model mailing list, but that list is not very active, so I'd like to try the general R mailing list. Sorry if anyone receives the double post. Hi, I have a dataset of animals receiving some eye treatments. There are 8 treatments, each animal's right and left eye was measured with some scores (ranging from 0 to 7) 4 times after treatment. So there are nesting groups eyes within animal. Dataset attached dat-read.table(dat.txt,sep='\t',header=T,row.names=1) dat$id-factor(dat$id) str(dat) 'data.frame': 640 obs. of 5 variables: $ score: int 0 2 0 7 4 7 0 2 0 7 ... $ id : Factor w/ 80 levels 1,3,6,10,..: 7 48 66 54 18 26 38 52 39 63 ... $ rep : int 1 1 1 1 1 1 1 1 1 1 ... $ eye : Factor w/ 2 levels L,R: 2 2 2 2 2 2 2 2 2 2 ... $ trt : Factor w/ 8 levels A,B,C,Control,..: 1 1 1 1 1 1 1 1 1 1 ... I fit a mixed model using both lmer() from lme4 package and lme() from nlme package: lmer(score~trt+(1|id/eye),dat) Linear mixed model fit by REML Formula: score ~ trt + (1 | id/eye) Data: dat AIC BIC logLik deviance REMLdev 446.7 495.8 -212.4430.9 424.7 Random effects: Groups NameVariance Std.Dev. eye:id (Intercept) 6.9208e+00 2.630742315798 id (Intercept) 1.4471e-16 0.00012030 Residual 1.8750e-02 0.136930641909 Number of obs: 640, groups: eye:id, 160; id, 80 summary(lme(score~trt, random=(~1|id/eye), dat)) Linear mixed-effects model fit by REML Data: dat AIC BIClogLik 425.1569 474.0947 -201.5785 Random effects: Formula: ~1 | id (Intercept) StdDev:1.873576 Formula: ~1 | eye %in% id (Intercept) Residual StdDev:1.896126 0.1369306 As you can see, the variance components estimates of random effects are quite different between the 2 model fits. From the data, I know that the variance component for id can't be near 0, which is what lmer() fit produced, so I think the lme() fit is correct while lmer() fit is off. This can also be seen from AIC, BIC etc. lme() fit has better values than lmer() fit. I guess this might be due to lmer() didn't converge very well, is there anyway to adjust to make lmer() converge better to get similar results as lme()? That's your guess... I'd be more careful about jumping to conclusions. If this is a balanced data set, perhaps you could supply the result of summary(aov(score~trt+Error(id/eye), data=dat)) The correct estimates should be computable from the ANOVA table. -- Peter Dalgaard Center for Statistics, Copenhagen Business School Phone: (+45)38153501 Email: pd@cbs.dk Priv: pda...@gmail.com __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] navel-gazing
I have been tinkering around with this for a bit, and I am proud to
share navel gazer 1.0.
If no arguments are passed, it will look up the top 50 authors on the
r-help list, for the given month in the given year. You can also
specify one or more months as a character vector (e.g., August or
c(August, September) ). The same goes for years. Thanks to some
help from Henrique (although I promise this was not the only reason I
wanted it), it will not try to pull a month beyond the current one.
You can also choose a different list (such as r-devel). If you have
the time, you can set argument entire = TRUE, which will look up every
month from whatever year(s) you specified (or the current year if you
did not). It will return a named list with each element corresponding
to one month. Also, by default it will create a dotplot in lattice
(though this may be turned off via plot = FALSE). Finally, you can
specify how many authors you want. It defaults to 50.
It is also available at here:
http://gist.github.com/584910
###
navel.gazer - function(month = NULL, year = NULL, entire = FALSE,
list = r-help, n = 50, plot = TRUE) {
# Ben Bolker came up with most of the code
# Henrique Dallazuanna provided an edit to the z - line of code
# Brian Diggs provided capwords() to properly count Peter Dalgaard
# Joshua Wiley adapted all of it to one function
if(is.null(month)) {
month - format(Sys.Date(), format = %B)
}
if(isTRUE(entire)) {
month - unique(months(as.Date(1:365, 2000-01-01)))
}
if(is.null(year)) {
year - format(Sys.Date(), format = %Y)
}
if(length(year) 1) {
tmp - vector(mode = list, length = length(year))
for(i in seq_along(year)) {
tmp[[i]] - paste(year[i], month, sep = -)
}
times - unlist(tmp)
} else {
times - paste(year, month, sep = -)
}
require(zoo)
times - sort(as.yearmon(times, %Y-%B))
current - as.yearmon(Sys.Date(), %Y-%m)
times - format(times[times = current], %Y-%B)
# Function to extract the names
# Originally by Ben Bolker
namefun - function(x) {
gsub(\\n,,gsub(^.+I,,gsub(/I.+$,,x)))
}
# Based on a suggestion by Brian Diggs
# Capitalizes the first letter of each word
capwords - function(s, strict = FALSE) {
cap - function(s) paste(toupper(substring(s,1,1)),
{s - substring(s,2); if(strict) tolower(s) else s},
sep = , collapse = )
sapply(strsplit(s, split = ), cap, USE.NAMES = !is.null(names(s)))
}
# Collects the author names for the relevant month and list
# from the R archives
# Originally by Ben Bolker
grabber - function(month, list, n) {
baseurl - https://stat.ethz.ch/pipermail/;
require(RCurl)
# z - getURL(paste(baseurl,list,/,month,/author.html,sep=))
z - getURL(paste(baseurl,list,/, month,/author.html,sep=),
ssl.verifypeer = FALSE)
zz - strsplit(z,LI)[[1]]
cnames - capwords(sapply(zz[3:(length(zz)-1)],namefun))
rr - rev(sort(table(cnames)))
output - rr[1:n]
return(output)
}
# Create dot plots of the number of posts
# lattice dotplot() code primarily by Ben Bolker
plotter - function(dat) {
require(lattice)
if(length(dat) 1) {
old.par - par(no.readonly = TRUE)
on.exit(par(old.par))
par(ask = TRUE)
}
for(i in seq_along(dat)) {
print(dotplot(~rev(dat[[i]]), xlab = Number of posts,
main = names(dat)[i]))
}
invisible()
}
numbers - lapply(times, function(x)
{grabber(month = x, list = list, n = n)})
names(numbers) - times
if(plot) {
plotter(dat = numbers)
}
return(numbers)
}
###
Two examples:
navel.gazer(year = 2009, entire = TRUE)
navel.gazer(month = September, year = 2007)
This basically works out to be a tribute to David Winsemius:
navel.gazer(n = 1, entire = TRUE)
Hope you get a bit of fun out of this. I certainly enjoyed writing it!
Josh
On Tue, Aug 17, 2010 at 1:10 PM, Henrique Dallazuanna www...@gmail.com wrote:
I think that gsub example on help page is more clear:
library(XML)
# could be used the XML package to get the names
cnames - gsub('\n', '', head(tail(sapply(getNodeSet(htmlParse(z, asText =
TRUE), //i), xmlValue), -3), -3))
gsub((\\w)(\\w*), \\U\\1\\L\\2, cnames, perl=TRUE)
On Tue, Aug 17, 2010 at 4:44 PM, Brian Diggs dig...@ohsu.edu wrote:
Since Peter Dalgaard is splitting his considerable contributions between
Peter Dalgaard and peter dalgaard, I made the following changes (which
shouldn't be a problem unless e e cummings becomes a regular poster):
# from base::chartr documentation
capwords - function(s, strict = FALSE) {
cap - function(s) paste(toupper(substring(s,1,1)),
{s - substring(s,2); if(strict) tolower(s) else s},
sep = , collapse = )
sapply(strsplit(s, split = ),
Re: [R] lmer() vs. lme() gave different variance component estimates
I confirm John's problems with lmer. I'm using R 2.11.1. on Windows XP. R m4 - lmer(score~trt+(1|id/eye),dat) R m4 Linear mixed model fit by REML Formula: score ~ trt + (1 | id/eye) Data: dat AIC BIC logLik deviance REMLdev 446.7 495.8 -212.4430.9 424.7 Random effects: Groups NameVariance Std.Dev. eye:id (Intercept) 6.9208e+00 2.6307e+00 id (Intercept) 1.4471e-16 1.2030e-08 Residual 1.8750e-02 1.3693e-01 Number of obs: 640, groups: eye:id, 160; id, 80 One other note--the variance components from asreml agree with *lme*: ma - asreml(score~trt , random=~id + id:eye, data=dat) R sqrt(ma$gammas * ma$sigma2) id!id.var id:eye!id.varR!variance 1.8735643 1.8961309 0.1369306 Kevin On Fri, Sep 17, 2010 at 3:50 PM, array chip arrayprof...@yahoo.com wrote: Thank you Peter. Actually 3 people from mixed model mailing list tried my code using lmer(). They got the same results as what I got from lme4(). So they couldn't replicate my lmer() results: Random effects: Groups NameVariance Std.Dev. eye:id (Intercept) 3.59531 1.89613 id (Intercept) 3.51025 1.87357 Residual 0.01875 0.13693 Number of obs: 640, groups: eye:id, 160; id, 80 The only difference they can think of is they are using Mac and FreeBSD while mine is PC. I can't imagine this can be the reason. I re-install lme4 package, but still got weird results with lmer(). Per your suggestion, here is the results for aov() summary(aov(score~trt+Error(id/eye), data=dat)) Error: id Df Sum Sq Mean Sq F valuePr(F) trt7 1353.6 193.378 4.552 0.0002991 *** Residuals 72 3058.7 42.482 --- Signif. codes: 0 *** 0.001 ** 0.01 * 0.05 . 0.1 1 Error: id:eye Df Sum Sq Mean Sq F value Pr(F) Residuals 80 115214.4 Error: Within Df Sum Sq Mean Sq F value Pr(F) Residuals 480 9 0.01875 As can be seen, thr within subject variance estimate (0.01875) is the same between aov, lmer and lme. But I am not sure how to relate results between aov and lmer/lme for the other 2 variance components (id and eye%in%id). Thanks John - Original Message From: Peter Dalgaard pda...@gmail.com To: array chip arrayprof...@yahoo.com Cc: r-help@r-project.org Sent: Fri, September 17, 2010 1:05:27 PM Subject: Re: [R] lmer() vs. lme() gave different variance component estimates On 09/17/2010 09:14 PM, array chip wrote: Hi, I asked this on mixed model mailing list, but that list is not very active, so I'd like to try the general R mailing list. Sorry if anyone receives the double post. Hi, I have a dataset of animals receiving some eye treatments. There are 8 treatments, each animal's right and left eye was measured with some scores (ranging from 0 to 7) 4 times after treatment. So there are nesting groups eyes within animal. Dataset attached dat-read.table(dat.txt,sep='\t',header=T,row.names=1) dat$id-factor(dat$id) str(dat) 'data.frame': 640 obs. of 5 variables: $ score: int 0 2 0 7 4 7 0 2 0 7 ... $ id : Factor w/ 80 levels 1,3,6,10,..: 7 48 66 54 18 26 38 52 39 63 ... $ rep : int 1 1 1 1 1 1 1 1 1 1 ... $ eye : Factor w/ 2 levels L,R: 2 2 2 2 2 2 2 2 2 2 ... $ trt : Factor w/ 8 levels A,B,C,Control,..: 1 1 1 1 1 1 1 1 1 1 ... I fit a mixed model using both lmer() from lme4 package and lme() from nlme package: lmer(score~trt+(1|id/eye),dat) Linear mixed model fit by REML Formula: score ~ trt + (1 | id/eye) Data: dat AIC BIC logLik deviance REMLdev 446.7 495.8 -212.4430.9 424.7 Random effects: Groups NameVariance Std.Dev. eye:id (Intercept) 6.9208e+00 2.630742315798 id (Intercept) 1.4471e-16 0.00012030 Residual 1.8750e-02 0.136930641909 Number of obs: 640, groups: eye:id, 160; id, 80 summary(lme(score~trt, random=(~1|id/eye), dat)) Linear mixed-effects model fit by REML Data: dat AIC BIClogLik 425.1569 474.0947 -201.5785 Random effects: Formula: ~1 | id (Intercept) StdDev:1.873576 Formula: ~1 | eye %in% id (Intercept) Residual StdDev:1.896126 0.1369306 As you can see, the variance components estimates of random effects are quite different between the 2 model fits. From the data, I know that the variance component for id can't be near 0, which is what lmer() fit produced, so I think the lme() fit is correct while lmer() fit is off. This can also be seen from AIC, BIC etc. lme() fit has better values than lmer() fit. I guess this might be due to lmer() didn't converge very well, is there anyway to adjust to make lmer() converge better to get similar results as lme()? That's your guess... I'd be more careful about jumping to conclusions. If this is a balanced data set, perhaps you could supply the result of
Re: [R] Data Cube in R from CSV
(This is my first post -- I hope I am doing this right) Why not use an array? An array can be indexed in as many dimensions as you would like, and do not require any extra packages. x = array(1:27, dim = c(3, 3, 3)) x x[1, , ] x[ , 1, ] x[ , , 1] -David A. Johnston -- View this message in context: http://r.789695.n4.nabble.com/Data-Cube-in-R-from-CSV-tp2544404p2544486.html Sent from the R help mailing list archive at Nabble.com. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Is there a bisection method in R?
Here is something simple (does not have any checks for bad input), yet
should be adequate:
bisect - function(fn, lower, upper, tol=1.e-07, ...) {
f.lo - fn(lower, ...)
f.hi - fn(upper, ...)
feval - 2
if (f.lo * f.hi 0) stop(Root is not bracketed in the specified interval
\n)
chg - upper - lower
while (abs(chg) tol) {
x.new - (lower + upper) / 2
f.new - fn(x.new, ...)
if (abs(f.new) = tol) break
if (f.lo * f.new 0) upper - x.new
if (f.hi * f.new 0) lower - x.new
chg - upper - lower
feval - feval + 1
}
list(x = x.new, value = f.new, fevals=feval)
}
# An example
fn1 - function(x, a) {
exp(-x) - a*x
}
bisect(fn1, 0, 2, a=1)
bisect(fn1, 0, 2, a=2)
Ravi.
-Original Message-
From: r-help-boun...@r-project.org [mailto:r-help-boun...@r-project.org] On
Behalf Of Peter Dalgaard
Sent: Friday, September 17, 2010 4:16 PM
To: Gregory Gentlemen
Cc: r-help@r-project.org
Subject: Re: [R] Is there a bisection method in R?
On 09/17/2010 09:28 PM, Gregory Gentlemen wrote:
If uniroot is not a bisection method, then what function in R does use
bisection?
Why do you assume that there is one? uniroot contains a better algorithm
for finding bracketed roots.
It shouldn't be too hard to roll your own if you need one for
pedagogical purposes.
--
Peter Dalgaard
Center for Statistics, Copenhagen Business School
Phone: (+45)38153501
Email: pd@cbs.dk Priv: pda...@gmail.com
__
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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.
__
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PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
Re: [R] Matrix- create mean/min/max/stdev on column of matrix or rows?
See also the matrixStats package on CRAN. /Henrik On Fri, Sep 17, 2010 at 10:17 AM, Dennis Murphy djmu...@gmail.com wrote: Hi: Here's a simple example that you can tune to your needs: m - matrix(rpois(100, 10), nrow = 10) # Function to compute summary statistics: f - function(x) c(min = min(x), med = median(x), mean = mean(x), max = max(x)) # Apply to rows (index 1) apply(m, 1, f) [,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9] [,10] min 5.0 7.0 5.0 6.0 5.0 5.0 8.0 5.0 2.0 6.0 med 11.5 9.5 10.0 9.5 9.0 8.0 10.0 10.0 6.0 10.0 mean 11.1 9.8 10.4 10.3 9.6 7.6 10.5 9.3 6.6 9.8 max 15.0 14.0 17.0 15.0 17.0 10.0 14.0 14.0 16.0 12.0 # Apply to columns (index 2) apply(m, 2, f) [,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9] [,10] min 3.0 6.0 5.0 6.0 2.0 5.0 5.0 5.0 8.0 6.0 med 9.0 9.5 11.0 9.5 8.5 9.5 9.0 6.0 10.5 10.0 mean 8.6 9.6 10.8 9.8 8.5 9.7 9.7 7.8 11.0 9.5 max 12.0 15.0 15.0 17.0 14.0 15.0 17.0 14.0 16.0 14.0 HTH, Dennis On Fri, Sep 17, 2010 at 9:08 AM, Halabi, Anan anan.hal...@hp.com wrote: I made simulation with Weibull and create Matrix, How can I create mean/min/max/stdev on column or rows of matrix?, Thanks, __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] R Console - pasting into
For some reason, I have trouble pasting commands into the R Console (XP Pro and R v 2.11.1). This occurs mainly when copying from a PDF document and then pasting into the R Console. It will work for a while and then stop. It is difficult to identify what the sequence is prior to it not allowing further commands to be pasted into the R Console. Yes, the commands can be copied from the PDF into Notepad. However, after I have posted into the R Console for some time, it will not allow me to continue to do this, but I can type commands in (which can be frustrating when wanting to copy from another source). When it hangs, as described, I can still copy from the PDF into Notepad, but not from Notepad into the R Console, though I am still able to type commands in R Console. This means that it is not only a PDF but Notepad, which implies that the problem rests with the R Console. Any ideas would be welcomed. [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] how to import this kind of data?
Dear All, I am in a trouble with reading data. It is in txt file looking like this. 0.00632 18.00 2.310 0 0.5380 6.5750 65.20 4.0900 1 296.0 15.30 396.90 4.98 24.00 0.02731 0.00 7.070 0 0.4690 6.4210 78.90 4.9671 2 242.0 17.80 396.90 9.14 21.60 0.02729 0.00 7.070 0 0.4690 7.1850 61.10 4.9671 2 242.0 17.80 392.83 4.03 34.70 0.03237 0.00 2.180 0 0.4580 6.9980 45.80 6.0622 3 222.0 18.70 394.63 2.94 33.40 0.06905 0.00 2.180 0 0.4580 7.1470 54.20 6.0622 3 222.0 18.70 396.90 5.33 36.20 0.02985 0.00 2.180 0 0.4580 6.4300 58.70 6.0622 3 222.0 18.70 394.12 5.21 28.70 0.08829 12.50 7.870 0 0.5240 6.0120 66.60 5.5605 5 311.0 15.20 395.60 12.43 22.90 0.14455 12.50 7.870 0 0.5240 6.1720 96.10 5.9505 5 311.0 15.20 396.90 19.15 27.10 There are 14 variables. Therefore, the first of row should be at the end of the second row. So after importing the data, this should look like v1 v2v3 v4 v5v6 v7 v8 v9 v10 v11 v12v13v14 0.00632 18.00 2.310 0 0.5380 6.5750 65.20 4.0900 1 296.0 15.30 396.90 4.98 24.00 and so on. How can import this kind of data into R? Thank you, __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] How to compare, match two columns from diferent dataframe and assign values from one datafram to the other
Dear R experts, I'm new to R. It seems to be a simple question but I just can't find a way to do it. Please help me. I have two data sets x and y as shown in the following. I want to compare the first two columns in x and y, find the matched ones and assign the relative value from column 2 of y to generate the third column of x. Any help wil be appreciated. Thanks. x [,1] [,2] [1,] 1 0 [2,] 2 0 [3,] 3 0 [4,] 4 0 [5,] 5 0 [6,] 6 0 [7,] 7 0 [8,] 8 0 [9,] 9 0 [10,] 10 0 y [,1] [,2] [1,] 7 a [2,] 4 b [3,] 2 c [4,] 8 d [5,] 12 e [6,] 15 f The result I expect is: x [,1] [,2] [,3] [1,] 1 0 NA [2,] 2 0 c [3,] 3 0 NA [4,] 4 0 b [5,] 5 0 NA [6,] 6 0 NA [7,] 7 0 a [8,] 8 0 d [9,] 9 0 NA [10,] 10 0 NA Best, Ying __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] R Console - pasting into
Hi Troy, If you are using the R GUI for Windows, I highly recommend just copying and pasting everything into the accompanying script editor, and then you can run the commands you want directly from there. The Windows clipboard can be finicky sometimes, so I would not be too hasty to think the problem rests with the R console. You can also try pasting using the mouse (this is actually what you have to do with the Windows command prompt...), or using Shift+Insert as an alternate to Ctrl + v. Best of luck, Josh On Fri, Sep 17, 2010 at 2:57 PM, Troy Lynch tpl...@yahoo.com wrote: For some reason, I have trouble pasting commands into the R Console (XP Pro and R v 2.11.1). This occurs mainly when copying from a PDF document and then pasting into the R Console. It will work for a while and then stop. It is difficult to identify what the sequence is prior to it not allowing further commands to be pasted into the R Console. Yes, the commands can be copied from the PDF into Notepad. However, after I have posted into the R Console for some time, it will not allow me to continue to do this, but I can type commands in (which can be frustrating when wanting to copy from another source). When it hangs, as described, I can still copy from the PDF into Notepad, but not from Notepad into the R Console, though I am still able to type commands in R Console. This means that it is not only a PDF but Notepad, which implies that the problem rests with the R Console. Any ideas would be welcomed. [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. -- Joshua Wiley Ph.D. Student, Health Psychology University of California, Los Angeles http://www.joshuawiley.com/ __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] how to import this kind of data?
Soyeon -
I think scan() (combined with matrix and data.frame) is the
easiest way.
Suppose your text file is called data.txt. Then
data.frame(matrix(scan('data.txt'),byrow=TRUE,ncol=14))
should give you what you want.
- Phil Spector
Statistical Computing Facility
Department of Statistics
UC Berkeley
spec...@stat.berkeley.edu
On Fri, 17 Sep 2010, Soyeon Kim wrote:
Dear All,
I am in a trouble with reading data.
It is in txt file looking like this.
0.00632 18.00 2.310 0 0.5380 6.5750 65.20 4.0900 1 296.0 15.30
396.90 4.98 24.00
0.02731 0.00 7.070 0 0.4690 6.4210 78.90 4.9671 2 242.0 17.80
396.90 9.14 21.60
0.02729 0.00 7.070 0 0.4690 7.1850 61.10 4.9671 2 242.0 17.80
392.83 4.03 34.70
0.03237 0.00 2.180 0 0.4580 6.9980 45.80 6.0622 3 222.0 18.70
394.63 2.94 33.40
0.06905 0.00 2.180 0 0.4580 7.1470 54.20 6.0622 3 222.0 18.70
396.90 5.33 36.20
0.02985 0.00 2.180 0 0.4580 6.4300 58.70 6.0622 3 222.0 18.70
394.12 5.21 28.70
0.08829 12.50 7.870 0 0.5240 6.0120 66.60 5.5605 5 311.0 15.20
395.60 12.43 22.90
0.14455 12.50 7.870 0 0.5240 6.1720 96.10 5.9505 5 311.0 15.20
396.90 19.15 27.10
There are 14 variables. Therefore, the first of row should be at the
end of the second row.
So after importing the data, this should look like
v1 v2v3 v4 v5v6 v7 v8
v9 v10 v11 v12v13v14
0.00632 18.00 2.310 0 0.5380 6.5750 65.20 4.0900 1 296.0
15.30 396.90 4.98 24.00
and so on.
How can import this kind of data into R?
Thank you,
__
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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.
__
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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.
