Re: [R] Error Message using xyplot of lattice
Hi, You didn't provide a reproducible example. If your dataset is something like this: set.seed(495) DataSeries - data.frame(Date=seq(as.Date(2001-01-01),by=1 day, length.out=20), A= sample(10,20,replace=TRUE), B= rnorm(20)) ###Using your codes: Matrix_New1 - cbind(as.list(DataSeries[,Date]),as.list(DataSeries[,A]),colnames(DataSeries)[2]) Matrix_New2 - cbind(as.list(DataSeries[,Date]),as.list(DataSeries[,B]),colnames(DataSeries)[3]) str(Matrix_New1) #List of 60 str(Matrix_New2) #List of 60 Matrix_Complete- rbind(Matrix_New1,Matrix_New2) str(Matrix_Complete) #List of 120 Col_Names_MC-c(X,Y, Z) colnames(Matrix_Complete)-Col_Names_MC library(lattice) Plot_AB-xyplot(Y~ X, data =Matrix_Complete, type =c(l), groups=Z, as.table=TRUE, main=Development over time) #Error in eval(expr, envir, enclos) : object 'Z' not found #You could try: library(reshape2) DataSeriesM - setNames(melt(DataSeries,id.var=Date),LETTERS[c(24,26,25)]) xyplot(Y~X,data=DataSeriesM,type=l,groups=Z,as.table=TRUE,main=Development over time) #for a numeric X axis xyplot(Y~as.numeric(X),data=DataSeriesM,type=l,groups=Z,as.table=TRUE,main=Development over time) # with legends xyplot(Y~as.numeric(X),xlab=X,data=DataSeriesM,type=l,groups=Z,as.table=TRUE,main=Development over time,auto.key=list(x=.85, y=.95, border=TRUE,lines=TRUE)) Hope it helps. A.K. Hi everbody, I have the following error message occuring when I run my code: Error in eval(expr, envir, enclos) : object 'Series' not found The code I am using is the following: Matrix_New1 - cbind(as.list(DataSeries[,Date]),as.list(DataSeries[,A]),colnames(DataSeries)[2] ) Matrix_New2 - cbind(as.list(DataSeries[,Date]),as.list(DataSeries[,B]),colnames(DataSeries)[3] ) #whereas first and second columns should be numbers, third column is A and B respectively Matrix_Complete- rbind(Matrix_New1,Matrix_New2) Col_Names_MC-c(X,Y, Z) colnames(Matrix_Complete)-Col_Names_MC Plot_AB-xyplot(Y~ X, data =Matrix_Complete, type =c(l), groups=Z, as.table=TRUE, main=Development over time) print(Plot_AB) Can you explain me why this way of creating a plot is not working and what I Need to Change in order to be able to plot it? __ 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] 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%20Domicilios --they construct and analyze the sqlite-backed survey design that dr. lumley is referring to On Wed, Apr 2, 2014 at 6:58 PM, Thomas Lumley tlum...@uw.edu wrote: On Thu, Apr 3, 2014 at 2:37 AM, Leandro Marino leandromar...@leandromarino.com.br wrote: Dear R-Users, I was using survey for the past years and now I am experiencing some problems with scripts that was working in the past. We are working with big data bases so I can't put all variables that I will use in the svydesign. This was never supposed to work. The variables shouldn't take up any more room in the survey design object than they do anywhere else, but in any case the right solution when you have enough memory for the variables in a given analysis but not for all the variables in your dataset is to use the database-backed designs and put the data in something like SQLite. -thomas -- Thomas Lumley Professor of Biostatistics University of Auckland [[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] 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(datetimesequenz, format=%Y))) [1] 1960 1961 1962 1963 1964 1965 1966 1967 1968 1969 1970 1971 1972 [14] 1973 1974 ... ... [183] 2154 2155 2157 2158 2159 2160 2161 2162 2167 sessionInfo() R version 3.0.2 (2013-09-25) Platform: i386-w64-mingw32/i386 (32-bit) locale: [1] LC_COLLATE=English_Australia.1252 LC_CTYPE=English_Australia.1252 [3] LC_MONETARY=English_Australia.1252 LC_NUMERIC=C [5] LC_TIME=English_Australia.1252 attached base packages: [1] grDevices datasets splines graphics stats tcltk utils methods base other attached packages: [1] svSocket_0.9-55 TinnR_1.0-5 R2HTML_2.2.1Hmisc_3.12-2 Formula_1.1-1 [6] survival_2.37-4 loaded via a namespace (and not attached): [1] cluster_1.14.4 fortunes_1.5-0 grid_3.0.2 lattice_0.20-23 rpart_4.1-3 [6] svMisc_0.9-69 tools_3.0.2 Cheers, D. On Fri, 4 Apr 2014 14:19:09 -0700 David Winsemius dwinsem...@comcast.net wrote On Apr 4, 2014, at 9:54 AM, Duncan Murdoch wrote: On 04/04/2014 10:55 AM, Winkler, Matthias wrote: Dear R-users, I'm working on datasets which contain data from the years 1960 to 2100 .. I also produced a date/time-sequence in R, which showed the same mistakes (see example below). The mistakes occur at the same dates like in my datasets. It's always at the end of march. 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(datetimesequenz, format=%Y)))[1] 1960 1961 1962 ... [181] 2152 2153 2154 2156 2157 2158 2159 2160 2161 2166 Has anybody experienced the same problem and knows a workaround? I'm using R 3.0.1 under Windows 7 64bit. I also tried this with R 3.0.3, it showed the same problem. Thank you for your help! I don't see this in 3.1.0 beta. Do you? I'm not seeing it on a Mac in 3.0.2 either. max(datetimesequenz) [1] 2100-01-01 PST length(datetimesequenz) [1] 1227241 Duncan Murdoch David Winsemius Alameda, CA, USA __ 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. South Africas premier free email service - www.webmail.co.za Fight Crime And Corruption! http://www.anc.org.za/2014/manifesto/ __ 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] 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 horizontally? - I couldn't find it . . and there doesn't seem to be a horizontal equivalent? Thanks, Phil. -- Philip Rhoades GPO Box 3411 Sydney NSW 2001 Australia E-mail: p...@pricom.com.au __ 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] GGPLOT Question
add +coord_flip() at the end. Does that do it? On Sun, Apr 6, 2014 at 7:03 AM, Philip Rhoades p...@pricom.com.au 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_crossbar(aes(ymin = min, ymax = max, x = id, y = min), fill = blue, fatten = 0) - is there some way to get geom_crossbar to print horizontally? - I couldn't find it . . and there doesn't seem to be a horizontal equivalent? Thanks, Phil. -- Philip Rhoades GPO Box 3411 Sydney NSW 2001 Australia E-mail: p...@pricom.com.au __ 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. -- Stephen Sefick ** Auburn University Biological Sciences 331 Funchess Hall Auburn, Alabama 36849 ** sas0...@auburn.edu http://www.auburn.edu/~sas0025 ** Let's not spend our time and resources thinking about things that are so little or so large that all they really do for us is puff us up and make us feel like gods. We are mammals, and have not exhausted the annoying little problems of being mammals. -K. Mullis A big computer, a complex algorithm and a long time does not equal science. -Robert Gentleman [[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] 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 p...@pricom.com.au 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_crossbar(aes(ymin = min, ymax = max, x = id, y = min), fill = blue, fatten = 0) - is there some way to get geom_crossbar to print horizontally? - I couldn't find it . . and there doesn't seem to be a horizontal equivalent? Thanks, Phil. -- Philip Rhoades GPO Box 3411 Sydney NSW 2001 Australia E-mail: p...@pricom.com.au __ 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. -- Stephen Sefick ** Auburn University Biological Sciences 331 Funchess Hall Auburn, Alabama 36849 ** sas0...@auburn.edu http://www.auburn.edu/~sas0025 ** Let's not spend our time and resources thinking about things that are so little or so large that all they really do for us is puff us up and make us feel like gods. We are mammals, and have not exhausted the annoying little problems of being mammals. -K. Mullis A big computer, a complex algorithm and a long time does not equal science. -Robert Gentleman [[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. -- Philip Rhoades GPO Box 3411 Sydney NSW 2001 Australia E-mail: p...@pricom.com.au __ 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] 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? 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 p...@pricom.com.au 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_crossbar(aes(ymin = min, ymax = max, x = id, y = min), fill = blue, fatten = 0) - is there some way to get geom_crossbar to print horizontally? - I couldn't find it . . and there doesn't seem to be a horizontal equivalent? Thanks, Phil. -- Philip Rhoades GPO Box 3411 Sydney NSW 2001 Australia E-mail: p...@pricom.com.au __ 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. -- Stephen Sefick ** Auburn University Biological Sciences 331 Funchess Hall Auburn, Alabama 36849 ** sas0...@auburn.edu http://www.auburn.edu/~sas0025 ** Let's not spend our time and resources thinking about things that are so little or so large that all they really do for us is puff us up and make us feel like gods. We are mammals, and have not exhausted the annoying little problems of being mammals. -K. Mullis A big computer, a complex algorithm and a long time does not equal science. -Robert Gentleman [[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. -- Philip Rhoades GPO Box 3411 Sydney NSW 2001 Australia E-mail: p...@pricom.com.au __ 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] 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(Class = c(1L, 1L, 1L, 1L, 1L, 2L, 2L, 2L), sil = c(0.734, 0.734, 0.734, 0.734, 0.734, -0.03, -0.03, -0.03), M201.1637T.1 = c(-1.077019059, -1.025923945, -2.025907674, -1.223001413, -1.547348898, -0.376842603, -1.33495095, -0.486811653), M203.1794T.1 = c(-0.884899777, -0.878305283, -1.910526051, -1.446826543, -1.950515819, -0.192865129, -1.669691644, -0.636095942), M205.1950T.1 = c(-1.307163965, -1.022407192, -2.050283307, -1.508604131, -1.710170605, -0.197410826, -1.547129558, -0.780189201 ), M207.2107T.1 = c(-1.378614081, -0.950293267, -1.714837198, -1.827195011, -1.629677288, -0.064343778, -1.598304259, -0.502002575 )), .Names = c(Class, sil, M201.1637T.1, M203.1794T.1, M205.1950T.1, M207.2107T.1), class = data.frame, row.names = c(52T_D06_19_42, 500030X_B03_19_15, 500059R_G09_19_81, 500061V_H02_13_86, 500078W_D10_6_46, 500082M_D05_18_41, 500105S_B09_15_21, 500120W_B04_19_16) Thanks in advance Nico [[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] 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, type=source) checking for nc_create in -lnetcdf... no configure: error: netcdf library not found ERROR: configuration failed for package ‘RNetCDF’ * removing ‘/Library/Frameworks/R.framework/Versions/3.1/Resources/library/RNetCDF’ install.packages(ncdf, type=source) configure: error: netcdf header netcdf.h not found ERROR: configuration failed for package ‘ncdf’ * removing ‘/Library/Frameworks/R.framework/Versions/3.1/Resources/library/ncdf’ Warning in install.packages : installation of package ‘ncdf’ had non-zero exit status install.packages(ncdf4, type=source) ERROR: configuration failed for package ‘ncdf4’ * removing ‘/Library/Frameworks/R.framework/Versions/3.1/Resources/library/ncdf4’ Warning in install.packages : installation of package ‘ncdf4’ had non-zero exit status Sincerely, Marc Girondot __ 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] 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 certainly not wisdom. H. Gilbert Welch On Sun, Apr 6, 2014 at 7:23 AM, Nico Met nicome...@gmail.com wrote: 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(Class = c(1L, 1L, 1L, 1L, 1L, 2L, 2L, 2L), sil = c(0.734, 0.734, 0.734, 0.734, 0.734, -0.03, -0.03, -0.03), M201.1637T.1 = c(-1.077019059, -1.025923945, -2.025907674, -1.223001413, -1.547348898, -0.376842603, -1.33495095, -0.486811653), M203.1794T.1 = c(-0.884899777, -0.878305283, -1.910526051, -1.446826543, -1.950515819, -0.192865129, -1.669691644, -0.636095942), M205.1950T.1 = c(-1.307163965, -1.022407192, -2.050283307, -1.508604131, -1.710170605, -0.197410826, -1.547129558, -0.780189201 ), M207.2107T.1 = c(-1.378614081, -0.950293267, -1.714837198, -1.827195011, -1.629677288, -0.064343778, -1.598304259, -0.502002575 )), .Names = c(Class, sil, M201.1637T.1, M203.1794T.1, M205.1950T.1, M207.2107T.1), class = data.frame, row.names = c(52T_D06_19_42, 500030X_B03_19_15, 500059R_G09_19_81, 500061V_H02_13_86, 500078W_D10_6_46, 500082M_D05_18_41, 500105S_B09_15_21, 500120W_B04_19_16) Thanks in advance Nico [[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] 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 marc_...@yahoo.fr 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 for MacOSX (Marverick): These packages are RnetCDF, ncdf or ncdf4. For all, I get error when I try to install them: install.packages(RNetCDF, type=source) checking for nc_create in -lnetcdf... no configure: error: netcdf library not found ERROR: configuration failed for package ‘RNetCDF’ * removing ‘/Library/Frameworks/R.framework/Versions/3.1/Resources/library/RNetCDF’ install.packages(ncdf, type=source) configure: error: netcdf header netcdf.h not found ERROR: configuration failed for package ‘ncdf’ * removing ‘/Library/Frameworks/R.framework/Versions/3.1/Resources/library/ncdf’ Warning in install.packages : installation of package ‘ncdf’ had non-zero exit status install.packages(ncdf4, type=source) ERROR: configuration failed for package ‘ncdf4’ * removing ‘/Library/Frameworks/R.framework/Versions/3.1/Resources/library/ncdf4’ Warning in install.packages : installation of package ‘ncdf4’ had non-zero exit status Sincerely, Marc Girondot __ 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. -- Pascal Oettli Project Scientist JAMSTEC Yokohama, Japan __ 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] 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. Hopefully the exact package name will be obvious in the package manager on your system. Regards, --Dave On Sun, Apr 6, 2014 at 7:26 AM, Marc Girondot marc_...@yahoo.fr 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 for MacOSX (Marverick): These packages are RnetCDF, ncdf or ncdf4. For all, I get error when I try to install them: install.packages(RNetCDF, type=source) checking for nc_create in -lnetcdf... no configure: error: netcdf library not found ERROR: configuration failed for package 'RNetCDF' * removing '/Library/Frameworks/R.framework/Versions/3.1/ Resources/library/RNetCDF' install.packages(ncdf, type=source) configure: error: netcdf header netcdf.h not found ERROR: configuration failed for package 'ncdf' * removing '/Library/Frameworks/R.framework/Versions/3.1/ Resources/library/ncdf' Warning in install.packages : installation of package 'ncdf' had non-zero exit status install.packages(ncdf4, type=source) ERROR: configuration failed for package 'ncdf4' * removing '/Library/Frameworks/R.framework/Versions/3.1/ Resources/library/ncdf4' Warning in install.packages : installation of package 'ncdf4' had non-zero exit status Sincerely, Marc Girondot __ 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 W. Pierce Division of Climate, Atmospheric Science, and Physical Oceanography Scripps Institution of Oceanography, La Jolla, California, USA (858) 534-8276 (voice) / (858) 534-8561 (fax)dpie...@ucsd.edu [[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] 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 later talk about coloring and formatting... are you printing the matrix using Markdown or LaTeX? You cannot color data directly in R, only upon output. Are you plotting using a heatmap? You also mention comparing one column with multiple other columns. Regardless if this were Excel or not, that would be unclear. Do you want to compare sil with each column separately and create a whole new set of columns containing color names, or compare to the minimum of all columns and make a single column of color names for sil? I think you need to clarify your intent a bit more before I can help. --- 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. On April 6, 2014 7:23:56 AM PDT, Nico Met nicome...@gmail.com wrote: 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(Class = c(1L, 1L, 1L, 1L, 1L, 2L, 2L, 2L), sil = c(0.734, 0.734, 0.734, 0.734, 0.734, -0.03, -0.03, -0.03), M201.1637T.1 = c(-1.077019059, -1.025923945, -2.025907674, -1.223001413, -1.547348898, -0.376842603, -1.33495095, -0.486811653), M203.1794T.1 = c(-0.884899777, -0.878305283, -1.910526051, -1.446826543, -1.950515819, -0.192865129, -1.669691644, -0.636095942), M205.1950T.1 = c(-1.307163965, -1.022407192, -2.050283307, -1.508604131, -1.710170605, -0.197410826, -1.547129558, -0.780189201 ), M207.2107T.1 = c(-1.378614081, -0.950293267, -1.714837198, -1.827195011, -1.629677288, -0.064343778, -1.598304259, -0.502002575 )), .Names = c(Class, sil, M201.1637T.1, M203.1794T.1, M205.1950T.1, M207.2107T.1), class = data.frame, row.names = c(52T_D06_19_42, 500030X_B03_19_15, 500059R_G09_19_81, 500061V_H02_13_86, 500078W_D10_6_46, 500082M_D05_18_41, 500105S_B09_15_21, 500120W_B04_19_16) Thanks in advance Nico [[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] 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/tree/master/Pesquisa%20Nacional%20por%20Amostra%20de%20Domicilios --they construct and analyze the sqlite-backed survey design that dr. lumley is referring to Thank you for this and all of your other work aimed at improving access to governmental data resource. The script for importation of the SEER text data ran flawlessly. The link at the bottom of the page in the first link to Lumley's old page on database backed svy objects at UW is now at an r-forge hosted page: http://r-survey.r-forge.r-project.org/survey/svy-dbi.html -- David. On Wed, Apr 2, 2014 at 6:58 PM, Thomas Lumley tlum...@uw.edu wrote: On Thu, Apr 3, 2014 at 2:37 AM, Leandro Marino leandromar...@leandromarino.com.br wrote: Dear R-Users, I was using survey for the past years and now I am experiencing some problems with scripts that was working in the past. We are working with big data bases so I can't put all variables that I will use in the svydesign. This was never supposed to work. The variables shouldn't take up any more room in the survey design object than they do anywhere else, but in any case the right solution when you have enough memory for the variables in a given analysis but not for all the variables in your dataset is to use the database-backed designs and put the data in something like SQLite. -thomas -- Thomas Lumley Professor of Biostatistics University of Auckland [[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. David Winsemius, MD Alameda, CA, USA __ 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] 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 http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[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 the subsequent computations. The following is only that part of the code which fits the mixed effects model. I tried with tryCatch as shown below, but it's not serving my purpose. I guess something is wrong in my approach. ### grouped.data-groupedData(formula = conc ~ t | subject, data = data.d) model.d-nlme(conc~f2(dose,Theta1,Theta2,Theta3,t), fixed=Theta1+Theta2+Theta3~1, data=grouped.data, random=Theta1+Theta2+Theta3~1, start=list(fixed=ini.pkpara)) summ-summary(model.d) # summary of the model tryCatch(summ, error = function() next) ### Any suggestion will be more than great. Thank you very much. Regards, Jamil [[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] 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 not. How can this be? Browse[1] identical(shft$pk, shft_mat$pk) [1] TRUE Browse[1] identical(shft$newv_f13__bool, shft_mat$newv_f13__bool) [1] TRUE Browse[1] identical(shft, shft_mat) [1] FALSE I have attached a file in which the two data frames are saved (using the save() function). __ 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: 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 them does include the random effect to be tested and the other one does not. However, it is well known that the anova() function refits the models with ML (new versions also output a warning that they do so). But in the new version of anova() you can prevent anova() from doing so by setting the option refit=FALSE. In order to test for random effects should I set refit=FALSE in my call to anova() or not? If I do set refit=FALSE the p-values tend to be lower. (Additional question: Are the p-values calculated by anova() anti-conservative when I set refit=FALSE?) Thanks for any help __ 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] 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. 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? 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 p...@pricom.com.au 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_crossbar(aes(ymin = min, ymax = max, x = id, y = min), fill = blue, fatten = 0) - is there some way to get geom_crossbar to print horizontally? - I couldn't find it . . and there doesn't seem to be a horizontal equivalent? Thanks, Phil. -- Philip Rhoades GPO Box 3411 Sydney NSW 2001 Australia E-mail: p...@pricom.com.au __ 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. -- Stephen Sefick ** Auburn University Biological Sciences 331 Funchess Hall Auburn, Alabama 36849 ** sas0...@auburn.edu http://www.auburn.edu/~sas0025 ** Let's not spend our time and resources thinking about things that are so little or so large that all they really do for us is puff us up and make us feel like gods. We are mammals, and have not exhausted the annoying little problems of being mammals. -K. Mullis A big computer, a complex algorithm and a long time does not equal science. -Robert Gentleman [[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. -- Philip Rhoades GPO Box 3411 Sydney NSW 2001 Australia E-mail: p...@pricom.com.aupdf( paper=a4r, width=11, height=7 ) options(scipen=999) library(ggplot2) library(scales) df6 - read.table(text = Treatment min max \6 Surgical Cooling\ 0.01 0.2, header=TRUE) df5 - read.table(text = Treatment min max \5 Medical Cooling\ 0.01 2, header=TRUE) df4 - read.table(text = Treatment min max \4 Human Hibernation\ 0.01 14, header=TRUE) df3 - read.table(text = Treatment min max \3 Short Term Suspended Animation\ 0.1 100, header=TRUE) df2 - read.table(text = Treatment min max \2 Neural Archive Preservation\ 1 10, header=TRUE) df1 - read.table(text = Treatment min max \1 Cryonic Suspension (whole body)\ 10 10, header=TRUE) ggplot() + geom_crossbar( data = df1, aes( ymin = min, ymax = max, x = Treatment, y = min ), fill = red, fatten = 0 ) + geom_crossbar( data = df2, aes( ymin = min, ymax = max, x = Treatment, y = min ), fill = red, fatten = 0 ) + geom_crossbar( data = df3, aes( ymin = min, ymax = max, x = Treatment, y = min ), fill = orange, fatten = 0 ) + geom_crossbar( data = df4, aes( ymin = min, ymax = max, x = Treatment, y = min ), fill = orange, fatten = 0 ) + geom_crossbar( data = df5, aes( ymin = min, ymax = max, x = Treatment, y = min ), fill = green, fatten = 0 ) + geom_crossbar( data = df6, aes( ymin = min, ymax = max, x = Treatment, y = min ), fill = green, fatten = 0 ) + ylab( Days ) + scale_y_log10( breaks=c( 0.01, 0.1, 1.0, 10.0, 100.1, 1000.0, 1.0, 10.0 ), labels=c( 0.01, 0.1, 1.0, 10, 100, 1,000, 10,000, 100,000 ) ) + coord_flip() + ggtitle( Comparison of Medical Temperature Reduction Treatments ) __ 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] 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 0.400303
1 75 0.32 0.400303
1 13 0.399000 0.400303
1 20 0.40 0.400303
2 219 0.393000 0.353350
2 50 0.06 0.353350
2 213 0.39 0.353350
2 204 0.496100 0.353350
2 19 0.393000 0.353350
2 201 0.388000 0.353350
I've tried:
pp$meanmm - with(pp, ave(pp[,3:4], Plan, FUN = mean))
People should do some 'dimensional analysis' when they get errors.
(And they should report the text of the errors.) The length and width
of what is specified on the LHS should be the same as what would be
produced on the RHS of hte assignment. But that would not have been
the first error that was encountered. You tried to pass two columns as
the first argument to a function that expected one, and then you tried
to assign the result to one column. This might have a better chance.
pp[ c('mean.m1' , 'mean.m2') ] - lapply( pp[ , 3:4] , function(x)
ave(x, pp$Plan, FUN=mean) )
pp
Plan X mm mm2 mean.m1 mean.m2
1 1 95 0.323000 0.400303 0.400303 0.400303
2 1 275 0.341818 0.400303 0.400303 0.400303
3 1 2 0.618000 0.400303 0.400303 0.400303
snipped
--
David.
But that doesn't seem to work.
On Sat, Apr 5, 2014 at 4:18 PM, David Winsemius dwinsem...@comcast.net
wrote:
On Apr 5, 2014, at 9:51 AM, Kate Ignatius wrote:
I'm trying to work out the average of a certain value by chromosome.
I've done the following, but it doesn't seem to work:
Say, I want to find average AD for chromosome 1 only and paste the
value next to all the positions on chromosome 1:
[sam$chrom == '1'] -
(sam$ad)/(colSums(sam[c(1:nrow(sam$chrom=='1'))],))
It looks wrong to me because of the mismatching lengths of the
lhs and rhs but since you have not provided a test dataset that's
all I will say.
The usual way to calculate a function within categorical groupings
that will be re-inserted alongside the original dataframe is to
use `ave`:
sam$mmad - with( sam, ave(ad, chrom, FUN=mean) )
I know this is convoluted and possible wrong... but I would like
to do
this for all chromosomes.
Thanks!
--
David Winsemius
Alameda, CA, USA
David Winsemius, MD
Alameda, CA, USA
David Winsemius, MD
Alameda, CA, USA
__
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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] 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() function, yet the data frames themselves are not. How can this be? Browse[1] identical(shft$pk, shft_mat$pk) [1] TRUE Browse[1] identical(shft$newv_f13__bool, shft_mat$newv_f13__bool) [1] TRUE Browse[1] identical(shft, shft_mat) [1] FALSE It could be as simple as having a different column order: df1 - df4 identical(df1,df4) [1] TRUE df1[] - df1[rev(names(df1))] identical(df1,df4) [1] FALSE I have attached a file in which the two data frames are saved (using the save() function). No attachment. Probably not a text file. Read the general instructions page more carefully. -- David Winsemius, MD Alameda, CA, USA __ 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] 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 thanoon.youni...@gmail.com: 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 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] 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 Coulombe patrick.coulo...@gmail.com wrote: 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 thanoon.youni...@gmail.com: 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 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. Don McKenzie Research Ecologist Pacific Wildland Fire Sciences Lab US Forest Service Affiliate Professor School of Environmental and Forest Sciences University of Washington d...@uw.edu [[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] 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 __ 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] 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. doing this looks good, however I tried to adapt to code in order to be able to plot more than just 2 time series and I again get some Errors. using this: DataSeriesM - setNames(melt(DataSeries,id.var=Date),LETTERS[c(24,18,19,20,21,22,23,26,25)]) where DataSeries has 5000 observations of 9 variables, I get the error message: Error in setNames(melt(DataSeries, id.var = Date), LETTERS[c(24, 18, : 'names' attribute [9] must be the same length as the vector [3] If I run this: length(LETTERS[c(24,18,19,20,21,22,23,26,25)]) length(DataSeries) I get 9 for both. I don't really understand why it is not working, is there anything you see? Using your example, I tried this: set.seed(495) DataSeries - data.frame(Date=seq(as.Date(2001-01-01),by=1 day, length.out=20), A= sample(10,20,replace=TRUE), B= rnorm(20),C= rnorm(20)-1) DataSeriesM - setNames(melt(DataSeries,id.var=Date),LETTERS[c(24,26,25,22)]) which dives me the same error message. How do I Need to adapt this part as well as the code below to plot more than 2 lines? # with legends xyplot(Y~as.numeric(X),xlab=X,data=DataSeriesM,type=l,groups=Z,as.table=TRUE,main=Development over time,auto.key=list(x=.85, y=.95, border=TRUE,lines=TRUE)) On Sunday, April 6, 2014 2:14 AM, arun smartpink...@yahoo.com wrote: Hi, You didn't provide a reproducible example. If your dataset is something like this: set.seed(495) DataSeries - data.frame(Date=seq(as.Date(2001-01-01),by=1 day, length.out=20), A= sample(10,20,replace=TRUE), B= rnorm(20)) ###Using your codes: Matrix_New1 - cbind(as.list(DataSeries[,Date]),as.list(DataSeries[,A]),colnames(DataSeries)[2]) Matrix_New2 - cbind(as.list(DataSeries[,Date]),as.list(DataSeries[,B]),colnames(DataSeries)[3]) str(Matrix_New1) #List of 60 str(Matrix_New2) #List of 60 Matrix_Complete- rbind(Matrix_New1,Matrix_New2) str(Matrix_Complete) #List of 120 Col_Names_MC-c(X,Y, Z) colnames(Matrix_Complete)-Col_Names_MC library(lattice) Plot_AB-xyplot(Y~ X, data =Matrix_Complete, type =c(l), groups=Z, as.table=TRUE, main=Development over time) #Error in eval(expr, envir, enclos) : object 'Z' not found #You could try: library(reshape2) DataSeriesM - setNames(melt(DataSeries,id.var=Date),LETTERS[c(24,26,25)]) xyplot(Y~X,data=DataSeriesM,type=l,groups=Z,as.table=TRUE,main=Development over time) #for a numeric X axis xyplot(Y~as.numeric(X),data=DataSeriesM,type=l,groups=Z,as.table=TRUE,main=Development over time) # with legends xyplot(Y~as.numeric(X),xlab=X,data=DataSeriesM,type=l,groups=Z,as.table=TRUE,main=Development over time,auto.key=list(x=.85, y=.95, border=TRUE,lines=TRUE)) Hope it helps. A.K. Hi everbody, I have the following error message occuring when I run my code: Error in eval(expr, envir, enclos) : object 'Series' not found The code I am using is the following: Matrix_New1 - cbind(as.list(DataSeries[,Date]),as.list(DataSeries[,A]),colnames(DataSeries)[2] ) Matrix_New2 - cbind(as.list(DataSeries[,Date]),as.list(DataSeries[,B]),colnames(DataSeries)[3] ) #whereas first and second columns should be numbers, third column is A and B respectively Matrix_Complete- rbind(Matrix_New1,Matrix_New2) Col_Names_MC-c(X,Y, Z) colnames(Matrix_Complete)-Col_Names_MC Plot_AB-xyplot(Y~ X, data =Matrix_Complete, type =c(l), groups=Z, as.table=TRUE, main=Development over time) print(Plot_AB) Can you explain me why this way of creating a plot is not working and what I Need to Change in order to be able to plot it? __ 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] 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 = ad, 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 = mad), colour = blue, size=0.75, show_guide = TRUE) + geom_hline(aes(yintercept = mmad, linetype = mmad), colour = black, size=0.75, show_guide = TRUE) + facet_wrap(~ Plan, scales = free, ncol = 4) + scale_linetype_manual(name = Plan of Health Care, values = c(mad = 1, mmad = 1),guide = legend) I'm sure I've over written something here... just not sure where (am new to ggplot) Data: Plan ad X m mad mmad 1 1 95 0.323000 0.400303 0.12 1 2 275 0.341818 0.400303 0.12 1 3 2 0.618000 0.400303 0.12 1 4 75 0.32 0.400303 0.12 1 5 13 0.399000 0.400303 0.12 1 6 20 0.40 0.400303 0.12 2 1 219 0.393000 0.353350 0.45 2 2 50 0.06 0.353350 0.45 2 3 213 0.39 0.353350 0.45 2 4 204 0.496100 0.353350 0.45 2 5 19 0.393000 0.353350 0.45 2 6 201 0.388000 0.353350 0.45 Plan goes up to 40, but I've only included a snippet of data here... __ 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] 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 06, 2014 8:26 AM To: r-help@r-project.org Subject: [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 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] 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 the data frames themselves are not. How can this be? Browse[1] identical(shft$pk, shft_mat$pk) [1] TRUE Browse[1] identical(shft$newv_f13__bool, shft_mat$newv_f13__bool) [1] TRUE Browse[1] identical(shft, shft_mat) [1] FALSE I have attached a file in which the two data frames are saved (using the save() function). Attachment did not come through. What does all.equal() say about your two data frames? cheers, Rolf Turner __ 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] 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='red', b='orange', c='green'), guid='none') +
ylab( Days ) +
scale_y_log10( breaks=c( 0.01, 0.1, 1.0, 10.0, 100.1, 1000.0,
1.0, 10.0 ), labels=c( 0.01, 0.1, 1.0, 10, 100,
1,000, 10,000, 100,000 ) ) +
coord_flip() +
ggtitle( Comparison of Medical Temperature Reduction Treatments )
On 7 April 2014 03:38, Philip Rhoades p...@pricom.com.au wrote:
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.
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?
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 p...@pricom.com.au
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_crossbar(aes(ymin = min, ymax = max, x = id, y = min),
fill = blue, fatten = 0)
- is there some way to get geom_crossbar to print horizontally? - I
couldn't find it . . and there doesn't seem to be a horizontal
equivalent?
Thanks,
Phil.
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E-mail: p...@pricom.com.au
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Stephen Sefick
**
Auburn University
Biological Sciences
331 Funchess Hall
Auburn, Alabama
36849
**
sas0...@auburn.edu
http://www.auburn.edu/~sas0025
**
Let's not spend our time and resources thinking about things that are so
little or so large that all they really do for us is puff us up and make
us
feel like gods. We are mammals, and have not exhausted the annoying
little
problems of being mammals.
-K. Mullis
A big computer, a complex algorithm and a long time does not equal
science.
-Robert Gentleman
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Yvan Richard
DRAGONFLY Science
Physical address: Level 5, 158 Victoria St, Te Aro, Wellington
Postal address: PO Box 27535, Wellington 6141
New Zealand
Ph: 04.385.9285
web page
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[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 = mad), colour = blue, size=0.75, show_guide = TRUE) + geom_hline(aes(yintercept = mmad, linetype = mmad), colour = black, size=0.75, show_guide = TRUE) + facet_wrap(~ Plan, scales = free, ncol = 4) + scale_linetype_manual(name = Plan of Health Care, values = c(mad = 1, mmad = 1),guide = legend) For this data: Data: Plan Person X m mad mmad 1 1 95 0.323000 0.400303 0.12 1 2 275 0.341818 0.400303 0.12 1 3 2 0.618000 0.400303 0.12 1 4 75 0.32 0.400303 0.12 1 5 13 0.399000 0.400303 0.12 1 6 20 0.40 0.400303 0.12 2 7 219 0.393000 0.353350 0.45 2 8 50 0.06 0.353350 0.45 2 9 213 0.39 0.353350 0.45 2 15 204 0.496100 0.353350 0.45 2 19 19 0.393000 0.353350 0.45 2 24 201 0.388000 0.353350 0.45 3 30 219 0.567 0.1254 0.89 3 14 50 0.679 0.1254 0.89 3 55 213 0.1234 0.1254 0.89 3 18 204 0.6135 0.1254 0.89 3 59 19 0.39356 0.1254 0.89 3 101 201 0.300 0.1254 0.89 I'm trying to manipulate the x axis using the following, only because the data can get very large and there is just way too many Persons to fit on the x-axis and I need to reduce it so its legible: scale_x_continuous(breaks = c(min(person), median(person), max(person)), labels = c(min(person), median(person), max(person))) However, given that I had to change `person` into a factor to order the data properly, the above code does not work. I get the errors, depending on how I fiddle around with the code: Error: Discrete value supplied to continuous scale Error in Summary.factor(c(1L, 2L, 3L, 4L, 5L, 6L, 7L, 8L, 9L, 10L, 11L, : min not meaningful for factors Changing `person` to numeric does not work, as the accumulated `person` for the entire dataset will then be on each Plan figure panel, as opposed to the scale specific for each Plan. That is, the x-axis for each panel (Plan) should have a scale beginning from its lowest Person to its highest Person (ie Plan 1 should have an x-axis that goes from 1 to 6 but Plan 3 has one that goes from 14 to 101). Changing the Person to numeric, the x-axis for all panels starts at 1 and goes to 101. Is there a work around for this? __ 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] 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 to move to the next iteration ignoring all the subsequent computations. The following is only that part of the code which fits the mixed effects model. I tried with tryCatch as shown below, but it's not serving my purpose. I guess something is wrong in my approach. ### grouped.data-groupedData(formula = conc ~ t | subject, data = data.d) model.d-nlme(conc~f2(dose,Theta1,Theta2,Theta3,t), fixed=Theta1+Theta2+Theta3~1, data=grouped.data, random=Theta1+Theta2+Theta3~1, start=list(fixed=ini.pkpara)) summ-summary(model.d) # summary of the model tryCatch(summ, error = function() next) ### Hi Jamil, I think you have to pass the expression: nlme(conc~f2(dose,Theta1,Theta2,Theta3,t), fixed=Theta1+Theta2+Theta3~1, data=grouped.data, random=Theta1+Theta2+Theta3~1, start=list(fixed=ini.pkpara)) not the result of the expression. 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] 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 installed in order to compile the R packages. Hopefully the exact package name will be obvious in the package manager on your system. Thanks a lot for these infos. Here are the last news for my problem of installation package in 3.1: I have installed macport and then I have tried to install development version of netcdf library: sudo port install netcdf-devel Error: Port netcdf-devel not found The netcdf library is available in macport but not the development one. In the meantime, I have tried to install ncdf and ncdf4 package after downloading the MacosX binary versions at: http://cran.r-project.org/bin/macosx/contrib/r-release/ncdf_1.6.6.tgz http://cran.r-project.org/bin/macosx/contrib/r-release/ncdf4_1.10.tgz I have installed both using the install_local() function of the package devtools. Both install and run correctly. The same procedure applied to RNetCDF (http://cran.r-project.org/web/packages/RNetCDF/index.html) has produced an error during installation. I have installed other packages in 3.1, or directly using install.packages() or loading the MacosX binary and using install_local(). I have still a problem with rgdal (http://cran.r-project.org/web/packages/rgdal/index.html). Probably again it is a problem of library (gdal) that is not present. I will wait that binary library is available in CRAN. Marc __ 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 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)),function(i)
{
par(mfrow=c(3,3)),
plot(dat1[,1],dat1[,i+1],
z[,i]-lm(dat1[,1]~dat1[,i+1]),
abline(z),
summary(z[,i])
}
here first column is dependent variable and other V2 to V10s are independent
variables. Also wanted look the summary (linear model) with each variable.
Thanks for your suggestions
KG
===
[[alternative HTML version deleted]]
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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 for a checklist. (And : You are mentioning both Windows7 and Linux distro which adds to the ambiguity and lack of clarity.). The README says the package needs compilation and provided details about how to go about that and who to contact with specific requests for information about your setup: http://cran.r-project.org/web/packages/multic/README Installation Error is related to Segmentation Fault. I did not save the error message, I wish I could post it here. gcc compiler version is 4.6.3 Also, there is no active support for windows binary version. Yes? The message linked to is a generic CRAN message. What is the point of mentioning this? I mentioned it, because the multic package is a unix/linux library. There is no support for Windows PC. I thought any one might provide support for multic package on windows PC. Could any one please help me install multic package on ubuntu 12.04, 64 bit system running with R 2.14.2 version. I'm not a Linux user so probably am speaking out of place and only doing so because it is the weekend and I've noticed that the traffic is slow on the mailing list on weekends. I believe Ubuntu is a fork of Debian so you may want to pay particular attention to mentions of Debian specific instructions in the links below. Many of the questions I have seen on R help from ubuntu users who have difficulties with installing packages get resolved by re-installing R using the development version of R. I have seen the use of r-base-dev as a target. http://cran.r-project.org/doc/manuals/R-admin.html#Essential-and-useful-other-programs-under-a-Unix_002dalike http://cran.r-project.org/doc/manuals/R-admin.html#Installing-R-under-Unix_002daikes There is also a Debian R mailing list and the archives are at markmail (although I suspect those are not he official ones.) http://markmail.org/search/+list:org%2Er-project%2Er-sig-debian I fixed the installation issue on ubuntu 12.04, by rebooting my system and installed multic on a fresh R (2.14.1) session. It works well! Thanks Sathish From: Qiang Kou [q...@umail.iu.edu] Sent: Saturday, April 05, 2014 9:23 PM To: David Winsemius Cc: Srinivasan, Sathish K; r-help@r-project.org Subject: Re: [R] Multic for windows 7 and Ubuntu I have just test the package on Ubuntu 12.04, everything is OK. So please provide the error message on your computer. Best, KK On Sat, Apr 5, 2014 at 9:02 PM, David Winsemius dwinsem...@comcast.netmailto:dwinsem...@comcast.net wrote: On Apr 5, 2014, at 1:50 AM, Srinivasan, Sathish K wrote: Hi all, Does anyone have issues installing multic package (http://cran.r-project.org/web/packages/multic/index.html) on ubuntu. 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 for a checklist. (And : You are mentioning both Windows7 and Linux distro which adds to the ambiguity and lack of clarity.). The README says the package needs compilation and provided details about how to go about that and who to contact with specific requests for information about your setup: http://cran.r-project.org/web/packages/multic/README Also, there is no active support for windows binary version. Yes? The message linked to is a generic CRAN message. What is the point of mentioning this? Could any one please help me install multic package on ubuntu 12.04, 64 bit system running with R 2.14.2 version. I'm not a Linux user so probably am speaking out of place and only doing so because it is the weekend and I've noticed that the traffic is slow on the mailing list on weekends. I believe Ubuntu is a fork of Debian so you may want to pay particular attention to mentions of Debian specific instructions in the links below. Many of the questions I have seen on R help from ubuntu users who have difficulties with installing packages get resolved by re-installing R using the development version of R. I have seen the use of r-base-dev as a target. http://cran.r-project.org/doc/manuals/R-admin.html#Essential-and-useful-other-programs-under-a-Unix_002dalike http://cran.r-project.org/doc/manuals/R-admin.html#Installing-R-under-Unix_002dalikes There is also a Debian R mailing list and the archives are at markmail (although I suspect those are not he official ones.) http://markmail.org/search/+list:org%2Er-project%2Er-sig-debian Thanks Sathish Please ... read. https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide
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 the error
message. Different results than expected? Then describe.
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)),function(i)
{
par(mfrow=c(3,3)),
plot(dat1[,1],dat1[,i+1],
z[,i]-lm(dat1[,1]~dat1[,i+1]),
What were you expecting to happen to dat1[,i+1] when i was at its
max?
abline(z),
summary(z[,i])
}
here first column is dependent variable and other V2 to V10s are
independent variables. Also wanted look the summary (linear model)
with each variable.
Thanks for your suggestions
KG
===
Please post in plain text.
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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=TRUE),ncol=10))
lapply(seq_len(ncol(dat1)),function(i)
{
par(mfrow=c(3,3)),
plot(dat1[,1],dat1[,i+1],
z[,i]-lm(dat1[,1]~dat1[,i+1]),
abline(z),
summary(z[,i])
}
here first column is dependent variable and other V2 to V10s are independent
variables. Also wanted look the summary (linear model) with each variable.
Thanks for your suggestions
KG
Hi Kristi,
You can get your plots like this:
for(i in 2:10) {
plot(dat1[,1],dat1[,i],ylab=paste(dat1[,,i,],sep=))
z-lm(dat1[,1]~dat1[,i])
abline(z)
print(summary(z))
}
This prints the summaries on the console. If you want to get a listing
with plots and summaries together, there are a number of ways, one of
which is the htmlize function in the prettyR package. Save the following
to a file named kg.R:
#title~Example listing with htmlize
z[[1]]-NULL
png(kg.png,width=600,height=600)
par(mfrow=c(3,3))
for(i in 2:10) {
plot(dat1[,1],dat1[,i],ylab=paste(dat1[,,i,],sep=))
z[[i]]-lm(dat1[,1]~dat1[,i])
abline(z[[i]])
}
dev.off()
for(i in 1:9) print(summary(z[[i]]))
then:
library(prettyR)
htmlize(kg.R)
Jim
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[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 good job normalising my reads. I am having the following issues: 1. I want to get the differentially expressed genes (DEGs) of my treatment not of my control. I don't understand after the eBayes analysis why I get the coefficients for both. I have tried a makeContrasts (TreatvsCont= c2-co, levels = design) to subtract the control effect but then I get 0 DEGs. 2. I am not sure when to include the 0 (null model) in the model formula, I have read examples for both types of models. This are my targets, with my column names of my counts, individual and condition targets Individual condition A1 1 co A2 3 co A4 4 co A5 5 co E1 1 c2 E2 2 c2 E3 3 c2 E4 4 c2 E5 5 c2 This is the code I have been trying: co2=as.matrix(read.table(2014_04_02_1h_PB.csv,header=T, sep=,, row.names=1)) nf = calcNormFactors (co2) targets= read.table (targets.csv, header = T, sep=,,row.names=1) treat - factor (targets$condition, levels= c(co, c2)) design - model.matrix(~0+treat) colnames (design) - levels (treat) y - voom(co2,design,lib.size=colSums(co2)*nf) corfit - duplicateCorrelation(y,design,block=targets$Individual) fit - lmFit(y,design,block=targets$Individual,correlation=corfit$consensus) fit2- eBayes (fit) results_trt - topTable (fit2, coef=c2, n=nrow (y), sort.by=none) From which gives me 18,000 genes with adj.P.Val 0.01 out of 22,000 genes that I have in total. Which makes no sense.. Thanks in advance for the help. [[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.
