Hello, I need to plot multiple confidence intervals for the same model parameter e.g. so for the same value of the parameter in point x_1 I would like to see four different confidence intervals so that I can compare the accuracy e.g. boot basic vs normal vs my own vs classic lm CI etc. I like very very much the plotCI implemented here: http://cran.r-project.org/web/packages/plotrix/index.html This is their example: library(plotrix) y <- runif(10) err <- runif(10) plotCI(x=1:10,y=y,uiw=err,liw=2*err,lwd=2,col="red",scol="blue",main="Add colors to the points and error bars") but does not seem to support plotting multiple CIs but only one per point, is there a similar library somewhere but having the possibility to plot multiple CIs? I know there is the function "segment" but I like this one above more :) Thanks in advance, Best regards, Giovanni
Hi Giovanni, I think the ggplot2 package might help you out here. Do you want something like this? library(ggplot2) data(mtcars) p <- ggplot(mtcars, aes(x=cyl, y=mpg)) p + stat_summary(fun.data = "mean_cl_boot", colour = "red", geom "errorbar") + stat_summary(fun.data = "mean_cl_normal", colour "blue", geom = "errorbar") ? See http://had.co.nz/ggplot2/stat_summary.html for details. -Ista On Fri, Apr 30, 2010 at 3:10 PM, Giovanni Azua <bravegag at gmail.com> wrote:> Hello, > > I need to plot multiple confidence intervals for the same model parameter e.g. so for the same value of the parameter in point x_1 I would like to see four different confidence intervals so that I can compare the accuracy e.g. boot basic vs normal vs my own vs classic lm CI etc. > > I like very very much the plotCI implemented here: > http://cran.r-project.org/web/packages/plotrix/index.html > > This is their example: > library(plotrix) > y <- runif(10) > err <- runif(10) > plotCI(x=1:10,y=y,uiw=err,liw=2*err,lwd=2,col="red",scol="blue",main="Add colors to the points and error bars") > > but does not seem to support plotting multiple CIs but only one per point, is there a similar library somewhere but having the possibility to plot multiple CIs? > > I know there is the function "segment" but I like this one above more :) > > Thanks in advance, > Best regards, > Giovanni > ______________________________________________ > R-help at r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/r-help > PLEASE do read the posting guide http://www.R-project.org/posting-guide.html > and provide commented, minimal, self-contained, reproducible code. >-- Ista Zahn Graduate student University of Rochester Department of Clinical and Social Psychology http://yourpsyche.org
Hello David, On Apr 30, 2010, at 6:00 PM, David Winsemius wrote:> Looks like you do not have the RTools bundle and perhaps not the XCode framework either? > > I am not suggesting that you do so, since it appears you are not conversant with compiling source code packages. If I am wrong about that point, then this is where you would get the gfortran compiler that Simon uses: > > http://r.research.att.com/tools/ > > My advice would be to go back to R.2.10.1 if you need Rcmdr. >I do have Xcode latest but not RTools. This below was my last failed attempt. Best regards, Giovanni> install.packages("Hmisc", dependencies=TRUE, type ="source")trying URL 'http://cran.ch.r-project.org/src/contrib/Hmisc_3.7-0.tar.gz' Content type 'application/x-gzip' length 563054 bytes (549 Kb) opened URL =================================================downloaded 549 Kb * installing *source* package ‘Hmisc’ ... ** libs ** arch - i386 gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -I/usr/local/include -fPIC -g -O2 -c Hmisc.c -o Hmisc.o gfortran -arch i386 -fPIC -g -O2 -c cidxcn.f -o cidxcn.o make: gfortran: No such file or directory make: *** [cidxcn.o] Error 1 ERROR: compilation failed for package ‘Hmisc’ * removing ‘/Library/Frameworks/R.framework/Versions/2.11/Resources/library/Hmisc’ The downloaded packages are in ‘/private/var/folders/5m/5mC0wYCSGMK8NbPZYhBEZE+++TI/-Tmp-/Rtmpz0R5nY/downloaded_packages’ Updating HTML index of packages in '.Library' Warning message: In install.packages("Hmisc", dependencies = TRUE, type = "source") : installation of package 'Hmisc' had non-zero exit status>[[alternative HTML version deleted]]
Hello, After installing gfortran from http://r.research.att.com/gfortran-4.2.3.dmg it finally works! see below. Thank you all. @Ista Zahn: Looks fantastic! :) thank you so much! ... is there a way to have a small circle on the true value? Best regards, Giovanni> install.packages("Hmisc", dependencies=TRUE, type ="source")trying URL 'http://cran.ch.r-project.org/src/contrib/Hmisc_3.7-0.tar.gz' Content type 'application/x-gzip' length 563054 bytes (549 Kb) opened URL =================================================downloaded 549 Kb * installing *source* package ?Hmisc? ... ** libs ** arch - i386 gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -I/usr/local/include -fPIC -g -O2 -c Hmisc.c -o Hmisc.o gfortran -arch i386 -fPIC -g -O2 -c cidxcn.f -o cidxcn.o gfortran -arch i386 -fPIC -g -O2 -c cidxcp.f -o cidxcp.o gfortran -arch i386 -fPIC -g -O2 -c hoeffd.f -o hoeffd.o gfortran -arch i386 -fPIC -g -O2 -c jacklins.f -o jacklins.o gfortran -arch i386 -fPIC -g -O2 -c largrec.f -o largrec.o gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -I/usr/local/include -fPIC -g -O2 -c mChoice.c -o mChoice.o gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -I/usr/local/include -fPIC -g -O2 -c nstr.c -o nstr.o gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -I/usr/local/include -fPIC -g -O2 -c ranksort.c -o ranksort.o gfortran -arch i386 -fPIC -g -O2 -c rcorr.f -o rcorr.o gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -I/usr/local/include -fPIC -g -O2 -c string_box.c -o string_box.o gfortran -arch i386 -fPIC -g -O2 -c wclosest.f -o wclosest.o gcc -arch i386 -std=gnu99 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/usr/local/lib -o Hmisc.so Hmisc.o cidxcn.o cidxcp.o hoeffd.o jacklins.o largrec.o mChoice.o nstr.o ranksort.o rcorr.o string_box.o wclosest.o -lgfortran -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation installing to /Library/Frameworks/R.framework/Versions/2.11/Resources/library/Hmisc/libs/i386 ** arch - x86_64 gcc -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/x86_64 -I/usr/local/include -fPIC -g -O2 -c Hmisc.c -o Hmisc.o gfortran -arch x86_64 -fPIC -g -O2 -c cidxcn.f -o cidxcn.o gfortran -arch x86_64 -fPIC -g -O2 -c cidxcp.f -o cidxcp.o gfortran -arch x86_64 -fPIC -g -O2 -c hoeffd.f -o hoeffd.o gfortran -arch x86_64 -fPIC -g -O2 -c jacklins.f -o jacklins.o gfortran -arch x86_64 -fPIC -g -O2 -c largrec.f -o largrec.o gcc -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/x86_64 -I/usr/local/include -fPIC -g -O2 -c mChoice.c -o mChoice.o gcc -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/x86_64 -I/usr/local/include -fPIC -g -O2 -c nstr.c -o nstr.o gcc -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/x86_64 -I/usr/local/include -fPIC -g -O2 -c ranksort.c -o ranksort.o gfortran -arch x86_64 -fPIC -g -O2 -c rcorr.f -o rcorr.o gcc -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/x86_64 -I/usr/local/include -fPIC -g -O2 -c string_box.c -o string_box.o gfortran -arch x86_64 -fPIC -g -O2 -c wclosest.f -o wclosest.o gcc -arch x86_64 -std=gnu99 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/usr/local/lib -o Hmisc.so Hmisc.o cidxcn.o cidxcp.o hoeffd.o jacklins.o largrec.o mChoice.o nstr.o ranksort.o rcorr.o string_box.o wclosest.o -lgfortran -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation installing to /Library/Frameworks/R.framework/Versions/2.11/Resources/library/Hmisc/libs/x86_64 ** R ** inst ** preparing package for lazy loading Loading required package: splines ** help *** installing help indices ** building package indices ... ** testing if installed package can be loaded * DONE (Hmisc) The downloaded packages are in ?/private/var/folders/5m/5mC0wYCSGMK8NbPZYhBEZE+++TI/-Tmp-/Rtmpz0R5nY/downloaded_packages? Updating HTML index of packages in '.Library'>
On 05/01/2010 12:10 AM, Giovanni Azua wrote:> Hello, > > I need to plot multiple confidence intervals for the same model parameter e.g. so for the same value of the parameter in point x_1 I would like to see four different confidence intervals so that I can compare the accuracy e.g. boot basic vs normal vs my own vs classic lm CI etc. > > I like very very much the plotCI implemented here: > http://cran.r-project.org/web/packages/plotrix/index.html > > This is their example: > library(plotrix) > y<- runif(10) > err<- runif(10) > plotCI(x=1:10,y=y,uiw=err,liw=2*err,lwd=2,col="red",scol="blue",main="Add colors to the points and error bars") > > but does not seem to support plotting multiple CIs but only one per point, is there a similar library somewhere but having the possibility to plot multiple CIs? > > I know there is the function "segment" but I like this one above more :) >Hi Giovanni, Have a look at the dispersion function. You could just call it four times with x positions stepped out as in the brkdn.plot or similar functions (see the example for brkdn.plot to see what I mean). Jim