Re: [R] solicit help to read in 384 plate color image

Hi There was package rimage which could read jpeg file in colours and manipulate with it. However it is not actively maintained and therefore it does not work in recent versions of R. I believe that R 2.14.0 is the last version able to use rimage. It was quite simple and I was tempted to start

Re: [R] How to plot data using ggplot

Hi > -Original Message- > From: r-help-boun...@r-project.org [mailto:r-help-bounces@r- > project.org] On Behalf Of drunkenphd > Sent: Friday, April 04, 2014 8:53 PM > To: r-help@r-project.org > Subject: Re: [R] How to plot data using ggplot > > djmuseR wrote > > Do you mean a continuous ra

[R] How to make a proper use of blocking in limma using voom

Hi all, I have a RNAseq data to analyse were I have a control and a one treatment for different individuals. I need to block the effects of the individual, but I am having several troubles to get the data that I need. I am using voom because my data is very heterogeneous and voom seams to do a goo

Re: [R] simple linear plots with a loop

On 04/07/2014 11:07 AM, Kristi Glover wrote: Hi R users, I was trying to plot with a fixed y with many independet variables. I tried this loop but it did not work. any suggestions? I wanted to make 9 plots. This is a just an example data. dat1<- as.data.frame(matrix(sample(1:20,100,replace=TR

Re: [R] simple linear plots with a loop

On Apr 6, 2014, at 6:07 PM, Kristi Glover wrote: Hi R users, I was trying to plot with a fixed y with many independet variables. It looks like you are plotting with a fixed x. I tried this loop but it did not work. any suggestions? Yes. Explain what "did not work" means. Error? Then post

Re: [R] Multic for windows 7 and Ubuntu

Thanks for your replies. > After doing a search on rhelp and r-sig-debian yours seems to be the first. > Shouldn't you be providing much more detail regarding your current setup and > versions of R and compilers, methods you are using, and the errors you are > getting? Review the Posting Guide

Re: [R] Any solution to have RnetCDF, ncdf or ncdf4 in R 3.1 ?

On Apr 6, 2014, at 4:21 PM, Marc Girondot wrote: Le 06/04/2014 16:47, David W. Pierce a écrit : Hi Marc, those packages are just interfaces to the netcdf library that must already exist on your machine. Try installing the netcdf library first, and then installing the R package. You will

[R] simple linear plots with a loop

Hi R users, I was trying to plot with a fixed y with many independet variables. I tried this loop but it did not work. any suggestions? I wanted to make 9 plots. This is a just an example data. dat1<- as.data.frame(matrix(sample(1:20,100,replace=TRUE),ncol=10)) lapply(seq_len(ncol(dat1)),funct

Re: [R] Any solution to have RnetCDF, ncdf or ncdf4 in R 3.1 ?

Le 06/04/2014 16:47, David W. Pierce a écrit : Hi Marc, those packages are just interfaces to the netcdf library that must already exist on your machine. Try installing the netcdf library first, and then installing the R package. You will need the development version of the netcdf library in

Re: [R] skipping an error message

On 04/06/2014 08:21 PM, Naser Jamil wrote: Dear R-user, May I seek your suggestion on an issue. I'm fitting non-linear mixed effects model as a part of my large R program. But sometimes I get error messages from it and the code stops working. In such cases, I want to skip the iterations and want

[R] Manipulating x axis using scale_x_continuous (but a factor is used). Is there a work around?

My code that I've used is: mcgc <- ggplot(sam, aes(x = person,y = m, colour = X)) + geom_point(size = 0.75) + scale_colour_gradient2(high="red", mid="green", limits=c(0,1), guide = "colourbar") + geom_hline(aes(yintercept = mad, linetype =

Re: [R] GGPLOT Question - #2

Hi Phil, You don't need multiple data frames. A single one will do. Try that. df <- rbind(df1, df2, df3, df4, df5, df6) df$type <- c('a','a','b','b','c','c') ggplot() + geom_crossbar(data = df, aes(ymin=min, ymax=max, x=Treatment, y=min, fill=type, fatten=0)) + scale_fill_manual(values=c(a

Re: [R] identical applied to data frames

On 07/04/14 02:00, Rguy wrote: I have two data frames that I believe are identical, yet checking them with identical() fails. Each data frame has two columns named 'pk' and 'newv_f13__bool'. As shown below, the columns of the data frames are identical, according to the identical() function, yet

Re: [R] structural equation models in R

Dear thanoon younis, RSiteSearch("structural equation model", "functions") turns up a number of relevant packages. I hope this helps, John > -Original Message- > From: r-help-boun...@r-project.org [mailto:r-help-bounces@r- > project.org] On Behalf Of thanoon younis > Sent: Sunday, April

[R] Colour of geom_hline is not correct in legend

I've used geom_point and geom_hline in ggplot2 and have gotten satisfactory legends for both. However, I have one black line and one blue line in the figure but in the legend they are both black - how can I correct this in the legend to be the right colors? mcgc <- ggplot(sam, aes(x = m,y = a

Re: [R] Error Message using xyplot of lattice

HI, Check the output of: datM <- melt(DataSeries,id.var="Date") head(datM,2)# 3 columns # Date variable value #1 2001-01-01 A 4 #2 2001-01-02 A 1 datM1 <- setNames(datM,LETTERS[c(24,26,25)]) library(lattice) xyplot(Y~as.numeric(X),data=datM1,groups=Z,type="l") A.K. hi, thank you for the help.

Re: [R] structural equation models in R

On Sun, 6 Apr 2014, Patrick Coulombe wrote: Not sure how we can help when you ask such a vague, broad question. But in any case, I would recommend using the package "lavaan" in R. Look it up: http://lavaan.ugent.be/ There's also plspm for Partial Least Squares -- Path Modeling. Rich __

Re: [R] structural equation models in R

There is also a newer package called “plspm” (“partial least squares path modeling”) http://cran.r-project.org/web/packages/plspm/plspm.pdf Even though it is called path modeling instead of SEM, it does seem to incorporate latent variables explicitly. On Apr 6, 2014, at 11:17 AM, Patrick Coulo

Re: [R] structural equation models in R

Hi Thanoon, Not sure how we can help when you ask such a vague, broad question. But in any case, I would recommend using the package "lavaan" in R. Look it up: http://lavaan.ugent.be/ Patrick 2014-04-06 6:26 GMT-06:00 thanoon younis : > hi > i need your help to know how can i analysis structural

Re: [R] identical applied to data frames

On Apr 6, 2014, at 7:00 AM, Rguy wrote: I have two data frames that I believe are identical, yet checking them with identical() fails. Each data frame has two columns named 'pk' and 'newv_f13__bool'. As shown below, the columns of the data frames are identical, according to the identical(

[R] Fwd: Recoding in R conditioned on a certain value.

On Apr 5, 2014, at 8:37 PM, Kate Ignatius wrote: Thanks, I ended up using this. I was curious how to get the mean of multiple columns by chrom (or Plan with the example below). Using this data for example: Plan X mm mm2 1 95 0.323000 0.400303 1 275 0.341818 0.400303 1 2 0.618000

Re: [R] GGPLOT Question - #2

People, On 2014-04-06 22:31, Philip Rhoades wrote: People, OK, the last two bits of the puzzle - can I colour the bars independently and change the scale from linear to logarithmic? To answer my own question - the attached file works for me but I guess could be improved? Thanks, Phil.

[R] identical applied to data frames

I have two data frames that I believe are identical, yet checking them with identical() fails. Each data frame has two columns named 'pk' and 'newv_f13__bool'. As shown below, the columns of the data frames are identical, according to the identical() function, yet the data frames themselves are no

[R] Question: Do I need to set refit=FALSE when testing for random effects with anova()?

Hello, I am currently testing whether I should include certain random effects in my lmer model or not. I use the anova function for that. My procedure so far is to fit the model with a function call to lmer() with REML=TRUE (the default option). Then I call anova() on the two models where one of t

[R] structural equation models in R

hi i need your help to know how can i analysis structural equation models in R. thanks alot [[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

[R] skipping an error message

Dear R-user, May I seek your suggestion on an issue. I'm fitting non-linear mixed effects model as a part of my large R program. But sometimes I get error messages from it and the code stops working. In such cases, I want to skip the iterations and want to move to the next iteration ignoring all th

Re: [R] Survey

On Apr 6, 2014, at 2:36 AM, Anthony Damico wrote: hi leandro, in case you're already familiar with ibge's pnad, you might find these examples useful-- http://www.asdfree.com/search/label/pesquisa%20nacional%20por%20amostra%20de%20domicilios%20%28pnad%29 https://github.com/ajdamico/usgsd/tre

Re: [R] Column value comparison and colouring

Your question confuses me. Perhaps you are still thinking as though this were Excel? You refer to "a big matrix", but your dput (thank you for that) is actually a data frame. Data frames are a list of columns, each of which can have a different type. "Clear them"? I think set them to NA. You l

Re: [R] Any solution to have RnetCDF, ncdf or ncdf4 in R 3.1 ?

Hi Marc, those packages are just interfaces to the netcdf library that must already exist on your machine. Try installing the netcdf library first, and then installing the R package. You will need the development version of the netcdf library installed in order to compile the R packages. Hopefull

Re: [R] Any solution to have RnetCDF, ncdf or ncdf4 in R 3.1 ?

Hello, Do you have NetCDF library correctly installed (with headers)? Regards, Pascal On Sun, Apr 6, 2014 at 11:26 PM, Marc Girondot wrote: > I just have installed the last RC of R 3.1. All is ok except for 3 packages > that I was not able to compile and they do not exist as precompiled package

Re: [R] Column value comparison and colouring

Post in plain text, not HTML. I would suggest that R is not Excel, and that you do not (shudder) treat it as such. Learn R and use it sensibly. Cheers, Bert Bert Gunter Genentech Nonclinical Biostatistics (650) 467-7374 "Data is not information. Information is not knowledge. And knowledge is ce

[R] Any solution to have RnetCDF, ncdf or ncdf4 in R 3.1 ?

I just have installed the last RC of R 3.1. All is ok except for 3 packages that I was not able to compile and they do not exist as precompiled package for MacOSX (Marverick): These packages are RnetCDF, ncdf or ncdf4. For all, I get error when I try to install them: install.packages("RNetCDF

[R] Column value comparison and colouring

Dear all, I have a big matrix, where I want to compare, one element of a vector with many others and clear them. For example: In column sil compare elements with other columns (0.734)>-1.0770 in 3rd column, so, color them bold else color them bold red For example: > dput(test) structure(list(C

Re: [R] GGPLOT Question - #2

People, OK, the last two bits of the puzzle - can I colour the bars independently and change the scale from linear to logarithmic? Thanks, Phil. On 2014-04-06 22:23, Philip Rhoades wrote: Stephen, On 2014-04-06 22:09, stephen sefick wrote: add +coord_flip() at the end. Does that do it?

Re: [R] GGPLOT Question

Stephen, On 2014-04-06 22:09, stephen sefick wrote: add +coord_flip() at the end. Does that do it? Wow! - that was a fast response! - yes that works - thanks a lot! Regards, Phil. On Sun, Apr 6, 2014 at 7:03 AM, Philip Rhoades wrote: People, I have this script: library(ggplot2) d

Re: [R] GGPLOT Question

add +coord_flip() at the end. Does that do it? On Sun, Apr 6, 2014 at 7:03 AM, Philip Rhoades wrote: > People, > > I have this script: > > library(ggplot2) > > df <- read.table(text = " id min max > Sp1 8.5 13.2 > Sp2 11.7 14.5 > Sp3 14.7 17.7 ", header=TRUE) > > ggplot(df) + > geom_crossba

[R] GGPLOT Question

People, I have this script: library(ggplot2) df <- read.table(text = " id min max Sp1 8.5 13.2 Sp2 11.7 14.5 Sp3 14.7 17.7 ", header=TRUE) ggplot(df) + geom_crossbar(aes(ymin = min, ymax = max, x = id, y = min), fill = "blue", fatten = 0) - is there some way to get geom_crossbar to print

Re: [R] Mistakes in date conversion for future date/time (POSIXct)

I _do_ see this error - on R 3.0.3 / Win XP however, not on R 2.11.1 / Linux. (Same hardware, 2 x OS, 2 x R versions) Maybe it's peculiar to to 'doze... datetimesequenz <- seq.POSIXt(from=as.POSIXct("1960-01-01 00:00"), to=as.POSIXct("2100-01-01 00:00"), by="1 hour") levels(as.factor(strftime(dat

Re: [R] Survey

hi leandro, in case you're already familiar with ibge's pnad, you might find these examples useful-- http://www.asdfree.com/search/label/pesquisa%20nacional%20por%20amostra%20de%20domicilios%20%28pnad%29 https://github.com/ajdamico/usgsd/tree/master/Pesquisa%20Nacional%20por%20Amostra%20de%20Domi