Re: [R] Fitting arbitrary curve to 1D data with error bars
Thanks, but if you have another closer look to my post, you will see that my question has nothing to do with drawing error bars on a plot. What I want is to do a curve fit to a data with error bars. Best, e. On 14 Nov 2013, at 04:21, Suzen, Mehmet wrote: If you are after adding error bars in a scatter plot; one example is given below : #some example data set.seed(42) df - data.frame(x = rep(1:10,each=5), y = rnorm(50)) #calculate mean, min and max for each x-value library(plyr) df2 - ddply(df,.(x),function(df) c(mean=mean(df$y),min=min(df$y),max=max(df$y))) #plot error bars library(Hmisc) with(df2,errbar(x,mean,max,min)) grid(nx=NA,ny=NULL) (From: http://stackoverflow.com/questions/13032777/scatter-plot-with-error-bars) __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Fitting arbitrary curve to 1D data with error bars
Maybe you are after weights option given by 'lm' or 'glm' See: http://stackoverflow.com/questions/6375650/function-for-weighted-least-squares-estimates On 14 November 2013 10:01, Erkcan Özcan erk...@hotmail.com wrote: Thanks, but if you have another closer look to my post, you will see that my question has nothing to do with drawing error bars on a plot. What I want is to do a curve fit to a data with error bars. Best, e. On 14 Nov 2013, at 04:21, Suzen, Mehmet wrote: If you are after adding error bars in a scatter plot; one example is given below : #some example data set.seed(42) df - data.frame(x = rep(1:10,each=5), y = rnorm(50)) #calculate mean, min and max for each x-value library(plyr) df2 - ddply(df,.(x),function(df) c(mean=mean(df$y),min=min(df$y),max=max(df$y))) #plot error bars library(Hmisc) with(df2,errbar(x,mean,max,min)) grid(nx=NA,ny=NULL) (From: http://stackoverflow.com/questions/13032777/scatter-plot-with-error-bars) __ 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] Fitting arbitrary curve to 1D data with error bars
Thanks, this was a useful pointer. Since the function I am trying to fit is exponential, I decided to use nls. And I was able to reproduce exactly the results and the plot in the URL I had posted. For future reference, here is the R code I wrote: require(gplots) xx - 1:10 yy - c(1.56,1.20,1.10,0.74,0.57,0.55,0.31,0.27,0.28,0.11) dy - c(0.02,0.02,0.20,0.03,0.03,0.10,0.05,0.02,0.10,0.05) plotCI(xx,yy,uiw=dy,gap=0) nlmod - nls(yy ~ Alpha * exp(Beta * xx), start=list(Alpha=1, Beta=-1)) lines(xx, predict(nlmod), col = blue) wnlmod - nls(yy ~ Alpha * exp(Beta * xx), start=list(Alpha=1, Beta=-1), weights=dy^-2) lines(xx, predict(wnlmod), col = red) Thanks to everybody who responded, e. On 14 Nov 2013, at 11:34, Suzen, Mehmet wrote: Maybe you are after weights option given by 'lm' or 'glm' See: http://stackoverflow.com/questions/6375650/function-for-weighted-least-squares-estimates On 14 November 2013 10:01, Erkcan Özcan erk...@hotmail.com wrote: Thanks, but if you have another closer look to my post, you will see that my question has nothing to do with drawing error bars on a plot. What I want is to do a curve fit to a data with error bars. Best, e. On 14 Nov 2013, at 04:21, Suzen, Mehmet wrote: If you are after adding error bars in a scatter plot; one example is given below : #some example data set.seed(42) df - data.frame(x = rep(1:10,each=5), y = rnorm(50)) #calculate mean, min and max for each x-value library(plyr) df2 - ddply(df,.(x),function(df) c(mean=mean(df$y),min=min(df$y),max=max(df$y))) #plot error bars library(Hmisc) with(df2,errbar(x,mean,max,min)) grid(nx=NA,ny=NULL) (From: http://stackoverflow.com/questions/13032777/scatter-plot-with-error-bars) __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Fitting arbitrary curve to 1D data with error bars
If you are after adding error bars in a scatter plot; one example is given below : #some example data set.seed(42) df - data.frame(x = rep(1:10,each=5), y = rnorm(50)) #calculate mean, min and max for each x-value library(plyr) df2 - ddply(df,.(x),function(df) c(mean=mean(df$y),min=min(df$y),max=max(df$y))) #plot error bars library(Hmisc) with(df2,errbar(x,mean,max,min)) grid(nx=NA,ny=NULL) (From: http://stackoverflow.com/questions/13032777/scatter-plot-with-error-bars) __ 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.
