Re: [R] Running multidimensional regressions

On Jan 13, 2014, at 4:28 PM, andrews Nikolaiv wrote: > > > > Dear R helpers!, > > I have a question on how to run a regression with many indices. > To give you a practical example, > > let > y_{itabp} be an dependent variable (representing prices) indexed by > i=country, t=time, a=area,

Re: [R] "squashed" domains when doing PCA with bio3d

Hi Bianca, If the domains are rotated between the trajectories, the motion cannot be captured by a single linear component. Think of projecting an arc on a straight line. You loose the (deflection) part on the second component. That looks like squashing. I've mentioned this in relation to MD simul

[R] "squashed" domains when doing PCA with bio3d

Hi everyone, I have been doing PCA using bio3d. My protein of interest has two domains and there are two crystal structures, one in a closed (domains are close together) and one in an open state (domains are nearly opposite each other). I ran MD simulations on both states and did PCA. When do

[R] Running multidimensional regressions

Dear R helpers!, I have a question on how to run a regression with many indices. To give you a practical example, let y_{itabp} be an dependent variable (representing prices) indexed by i=country, t=time, a=area, b=brand and p=package size. In particular, we collected prices on the pro

Re: [R] likelihood ratio test for mean difference assuming unequal variance

Amanda Li uchicago.edu> writes: > > Hello, > > I am so sorry, but I have been struggling with > the code for the entire day. > > I have a very simple dataset that looks like this: > response=c(45,47,24,35,47,56,29) > sub=c("A","A","B","B","C","C","C"£© > time=c(1,2,1,2,1,2,3) > gdata=cbind(re

Re: [R] Plot only a portion of a record

Hi Janet, You may also check library(xts).  mod.sage <- read.table(text="date year month day  wy  yd wyd  modQ 1 1965-10-01 1965    10  1 1966 274  1 0.3341630 2 1965-10-02 1965    10  2 1966 275  2 0.3223247 3 1965-10-03 1965    10  3 1966 276  3 0.3459057 4 1965-10-04 1965    10  4 1966 277

Re: [R] Plot only a portion of a record

On Jan 13, 2014, at 4:39 PM, Janet Choate wrote: > Hi R community, > i have a data frame of streamflow for 23 years, i.e. > >date year month day wy yd wyd modQ > 1 1965-10-01 196510 1 1966 274 1 0.3341630 > 2 1965-10-02 196510 2 1966 275 2 0.3223247 > 3 1965-10-03

Re: [R] Plot only a portion of a record

On 01/14/2014 11:39 AM, Janet Choate wrote: Hi R community, i have a data frame of streamflow for 23 years, i.e. date year month day wy yd wyd modQ 1 1965-10-01 196510 1 1966 274 1 0.3341630 2 1965-10-02 196510 2 1966 275 2 0.3223247 3 1965-10-03 196510 3 1

[R] Plot only a portion of a record

Hi R community, i have a data frame of streamflow for 23 years, i.e. date year month day wy yd wyd modQ 1 1965-10-01 196510 1 1966 274 1 0.3341630 2 1965-10-02 196510 2 1966 275 2 0.3223247 3 1965-10-03 196510 3 1966 276 3 0.3109057 i only want to plot 1 of

Re: [R] Barplot not showing all labels

If the problem is that not all y-axis labels fit on the horizontal barplot with the default settings, you can rotate then to horizontal with las=1 and reduce their size with cex.names=0.5 to avoid overlap, as in barplot(structure(1:50, names=state.name), horiz=TRUE,las=1, cex.names=0.5) or, usin

Re: [R] How to use ddply

On Jan 13, 2014, at 1:29 PM, Amitabh Dugar wrote: > I have never used R-help to pose a question to the R-users community; is > sending this Email the right way to do so? > > I am trying to use the ddply function in the plyr package to accomplish the > following: > I have a data frame of the ty

Re: [R] SE for R-squared

On 12 Jan 2014, at 21:36 , John C Frain wrote: > Have a look at > > http://davegiles.blogspot.ie/2013/10/more-on-distribution-of-r-squared.html > Or head directly for the Wikipedia page for the noncentral beta distribution (and/or noncentral F). Giles doesn't really do the non-null distribut

Re: [R] How to use ddply

Hi, Try: ddply(test,.(monthend_n),mutate,quintiles=cut(wgtdiff,5)) A.K. On Monday, January 13, 2014 5:32 PM, Amitabh Dugar wrote: I have never used R-help to pose a question to the R-users community; is sending this Email the right way to do so? I am trying to use the ddply function in the p

[R] likelihood ratio test for mean difference assuming unequal variance

Hello, I am so sorry, but I have been struggling with the code for the entire day. I have a very simple dataset that looks like this: response=c(45,47,24,35,47,56,29) sub=c("A","A","B","B","C","C","C"£© time=c(1,2,1,2,1,2,3) gdata=cbind(response,sub,time) Namely, for three subjects, each has 2 o

[R] How to use ddply

I have never used R-help to pose a question to the R-users community; is sending this Email the right way to do so? I am trying to use the ddply function in the plyr package to accomplish the following: I have a data frame of the type:      ticker monthend_n wgtdiff    ret 156      AA   1999022

Re: [R] coxph with time-dependent covariates

On Jan 13, 2014, at 10:50 AM, Phil Stevenson wrote: > I am using the coxph() function (from the 'survival' package) for a data > set that requires one of the covariates to be treated as time-dependent. > The issue is with this data set is there are some covariate values that are > missing at the t

Re: [R] Barplot not showing all labels

On 01/14/2014 06:15 AM, Jeff Johnson wrote: I have a table that consists of the following country codes and frequencies: AE AN AR AT AU BB BD BE BH BM BN BO BR BS CA CH CM CN CO CR CY DE DK DO EC ES 0 3 0 2 1 31 4 1 1 1 45 1 1 4 5 86 3 1 8 1 2 1 8 2 1 2 4 FI FR GB GR

[R] coxph with time-dependent covariates

I am using the coxph() function (from the 'survival' package) for a data set that requires one of the covariates to be treated as time-dependent. The issue is with this data set is there are some covariate values that are missing at the time point when the event occurs. For example: Person A: Da

[R] Barplot not showing all labels

I have a table that consists of the following country codes and frequencies: AE AN AR AT AU BB BD BE BH BM BN BO BR BS CA CH CM CN CO CR CY DE DK DO EC ES 0 3 0 2 1 31 4 1 1 1 45 1 1 4 5 86 3 1 8 1 2 1 8 2 1 2 4 FI FR GB GR GU HK ID IE IL IN IO IT JM JP KH KR KY LU LV MO

Re: [R] tcltk makes R crash under Mavericks

Dear Claudia, The R Commander installation notes at have some information (near the bottom) about trouble-shooting tcltk problems on Mac OS X. Maybe they will help. Best, John

Re: [R] tcltk makes R crash under Mavericks

On 13-01-2014, at 19:53, Claudia Tebaldi wrote: > Yes, thank you, as I said I did reinstall R and tcltk. That's not the > problem. > Look at what you wrote: "I tried reinstalling everything (R and the packages, and the tools' tcltk package -- even if I think it should be bundled with R by d

Re: [R] tcltk makes R crash under Mavericks

Yes, thank you, as I said I did reinstall R and tcltk. That's not the problem. For some reason loading the package still makes R crash. Claudia Tebaldi Project Scientist, CGD/NCAR and Science Fellow Climate Central (303) 497 1710 w (303) 775 5365 c On Mon, Jan 13, 2014 at 11:51 AM, Berend Has

Re: [R] tcltk makes R crash under Mavericks

On 13-01-2014, at 19:30, Claudia Tebaldi wrote: > Hello > > I was just forced to upgrade my OS X to Mavericks. Everything seemed to be > OK, R still worked seemingly fine within emacs (am using the latest > version, R 3.0.2, and the latest version of ESS, with Emacs 24.3.1) until I > tried load

[R] tcltk makes R crash under Mavericks

Hello I was just forced to upgrade my OS X to Mavericks. Everything seemed to be OK, R still worked seemingly fine within emacs (am using the latest version, R 3.0.2, and the latest version of ESS, with Emacs 24.3.1) until I tried loading the library extRemes. Apparently the call within that libra

Re: [R] R riddle

Hi, Try: dat1 <- read.table(text="I V3 X210505 X210505.1 X417802 X417802.1 X420385 X420385.1 X420480 X420480.1  A  A3205   B A   B A   B A   B A  M  A3662   A B   B B   A B   B B  M AR0012  

Re: [R] HOW TO CREATE A SUBSET FROM A LARGE DATASET based on some conditions

Hi, Try: dat1 <- read.table(text="2008 India ..  ..   .. .. .. 2009 India -   -   -   -   -  2010 India 5 1 6 0 -  2011 India 20 2 21 2 2 2012 India 35 4 42 3 5 2013 India 88 10 74 6  ..  2008 Brazil 3 2 .. .. 2 2009 Brazil 6 4 -   -   4",sep="",header=FALSE,stringsAsFactors=FALSE) dat2 <- dat1[

[R] Re. Confidence intervals for prediction with R2Bayesx

Hello, I am using the R2Bayesx package to fit a GAM to time-series data and then using this model to extrapolate beyond the extent of the time-series. The prediction.bayesx function works quite well to predict the series, but does not seem to provide uncertainty estimates for the prediction. The

Re: [R] Find the package of a class given classname

>> How to find the package of a class given classname? >> For example, there is a class called GAlignments, I want to do something >> like >> attr("GAlignments", "package") that gives you the package where the class >> is defined? But of course, attr("GAlignments", "package") won't work... > > You

Re: [R] computation

In this calculation: (dg0%*%t(dx0)) is [,1] [,2] [1,]0 -0.75 [2,]0 0.50 So: exp2 = NaN It is extremely easy to find out the issue if you go back line by line, this is a basic procedure of debugging. Please do it yourself next time. On Mon, Jan 13, 2014 at 3:09 PM, IZHAK shabso

[R] To modify FMCD

Dear R Experts, Can anyone teach me how to modify the FMCD algorithm in R. If I wish to replace the C-step in FMCD by the index set. Let I(old)={pi(1)old,pi(2)old,...,p(h)old} and I(new)={pi(1)new, pi(2)new,..,p(h)new} the index sets that correspond to the sample items in H(old) and H(new) res

Re: [R] tables package and alternative to col percent

On 14-01-13 12:02 AM, Daniel Cher wrote: Library "tables" and tabular function is neato. I'm trying to figure out how to get percents other than just row and columns. I'd like a percent of a factor. That's a recent addition, still only on R-forge. library(tables) c=data.frame(

Re: [R] computation

Hi Those have zero and dividing by zero produces NA > (dg0%*%t(dx0)) [,1] [,2] [1,]0 -0.75 [2,]0 0.50 > (dx0%*%t(dg0)) [,1] [,2] [1,] 0.00 0.0 [2,] -0.75 0.5 > NAs propagates in further computation. Regards Petr > -Original Message- > From: r-help-boun...@r-pro