Re: [R] xyplot: key inside the plot region / lme: confidence bands for predicted
On Wed, Jul 7, 2010 at 8:59 AM, Michael Friendly frien...@yorku.ca wrote: No one replied to my second question: how to get standard errors or confidence intervals for the estimated fixed effects from lme(). AFAICS, intervals() only gives CIs for coefficients. Assuming you mean 'predictions based on the estimated fixed effects' rather than 'estimated fixed effects', for one solution have a look at Ben Bolker's r-sig-mixed-models FAQ, about 2/3 of the way down: http://glmm.wikidot.com/faq Googling lme prediction intervals turns up quite a bit. Here's a recent conversation: http://comments.gmane.org/gmane.comp.lang.r.lme4.devel/3291 hope it helps, Kingsford Jones My working example is: library(nlme) library(lattice) Ortho - Orthodont Ortho$year - Ortho$age - 8 # make intercept = initial status Ortho.mix1 - lme(distance ~ year * Sex, data=Ortho, random = ~ 1 + year | Subject, method=ML) anova(Ortho.mix1) # get predicted values grid - expand.grid(year=0:6, Sex=c(Male, Female)) grid$age - grid$year+8 # plot vs. age fm.mix1 -cbind(grid, distance = predict(Ortho.mix1, newdata = grid, level=0)) xyplot(distance ~ age, data=fm.mix1, groups=Sex, type=b, par.settings = list(superpose.symbol = list(cex = 1.2, pch=c(15,16))), auto.key=list(text=levels(fm.mix1$Sex), points = TRUE, x=0.05, y=0.9, corner=c(0,1)), main=Linear mixed model: predicted growth) intervals(Ortho.mix1) Approximate 95% confidence intervals Fixed effects: lower est. upper (Intercept) 21.607212 22.615625 23.6240383 year 0.619660 0.784375 0.9490904 SexFemale -3.041252 -1.406534 0.2281834 year:SexFemale -0.562889 -0.304830 -0.0467701 attr(,label) [1] Fixed effects: Random Effects: Level: Subject lower est. upper sd((Intercept)) 1.0710615 1.7045122 2.712600 sd(year) 0.0281228 0.1541351 0.844783 cor((Intercept),year) -0.9358505 -0.0311195 0.927652 Within-group standard error: lower est. upper 1.07081 1.31004 1.60272 Peter Ehlers wrote: On 2010-07-02 9:37, Michael Friendly wrote: I have two questions related to plotting predicted values for a linear mixed model using xyplot: 1: With a groups= argument, I can't seem to get the key to appear inside the xyplot. (I have the Lattice book, but don't find an example that actually does this.) 2: With lme(), how can I generate confidence bands or prediction intervals around the fitted values? Once I get them, I'd like to add them to the plot. Example: library(nlme) library(lattice) Ortho - Orthodont Ortho$year - Ortho$year - 8 # make intercept = initial status Ortho.mix1 - lme(distance ~ year * Sex, data=Ortho, random = ~ 1 + year | Subject, method=ML, # correlation = corAR1 (form = ~ 1 | Subject) ) Ortho.mix1 # predicted values grid - expand.grid(year=0:6, Sex=c(Male, Female)) grid$age - grid$year+8 # plot vs. age fm.mix1 -cbind(grid, distance = predict(Ortho.mix1, newdata = grid, level=0)) xyplot(distance ~ age, data=fm.mix1, groups=Sex, type=b, pch=c(15,16), cex=1.2, auto.key=list(text=c(Male, Female), points = TRUE, x=8, y=26), main=Linear mixed model: predicted growth) Can someone help? -Michael Michael, the x,y location should be specified in the unit square (and you might want to set the 'corner' component). Ortho$year - Ortho$age - 8 ##fix typo xyplot(distance ~ age, data=fm.mix1, groups=Sex, type=b, pch=c(15,16), cex=1.2, auto.key=list(text=c(Male, Female), points = TRUE, x=0.1, y=0.8, corner=c(0,1))) See description of 'key' in ?xyplot. -Peter Ehlers -- Michael Friendly Email: friendly AT yorku DOT ca Professor, Psychology Dept. York University Voice: 416 736-5115 x66249 Fax: 416 736-5814 4700 Keele Street Web: http://www.datavis.ca Toronto, ONT M3J 1P3 CANADA __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] xyplot: key inside the plot region / lme: confidence bands for predicted
No one replied to my second question: how to get standard errors or confidence intervals for the estimated fixed effects from lme().AFAICS, intervals() only gives CIs for coefficients. My working example is: library(nlme) library(lattice) Ortho - Orthodont Ortho$year - Ortho$age - 8 # make intercept = initial status Ortho.mix1 - lme(distance ~ year * Sex, data=Ortho, random = ~ 1 + year | Subject, method=ML) anova(Ortho.mix1) # get predicted values grid - expand.grid(year=0:6, Sex=c(Male, Female)) grid$age - grid$year+8 # plot vs. age fm.mix1 -cbind(grid, distance = predict(Ortho.mix1, newdata = grid, level=0)) xyplot(distance ~ age, data=fm.mix1, groups=Sex, type=b, par.settings = list(superpose.symbol = list(cex = 1.2, pch=c(15,16))), auto.key=list(text=levels(fm.mix1$Sex), points = TRUE, x=0.05, y=0.9, corner=c(0,1)), main=Linear mixed model: predicted growth) intervals(Ortho.mix1) Approximate 95% confidence intervals Fixed effects: lower est. upper (Intercept)21.607212 22.615625 23.6240383 year0.619660 0.784375 0.9490904 SexFemale -3.041252 -1.406534 0.2281834 year:SexFemale -0.562889 -0.304830 -0.0467701 attr(,label) [1] Fixed effects: Random Effects: Level: Subject lower est.upper sd((Intercept))1.0710615 1.7045122 2.712600 sd(year) 0.0281228 0.1541351 0.844783 cor((Intercept),year) -0.9358505 -0.0311195 0.927652 Within-group standard error: lowerest. upper 1.07081 1.31004 1.60272 Peter Ehlers wrote: On 2010-07-02 9:37, Michael Friendly wrote: I have two questions related to plotting predicted values for a linear mixed model using xyplot: 1: With a groups= argument, I can't seem to get the key to appear inside the xyplot. (I have the Lattice book, but don't find an example that actually does this.) 2: With lme(), how can I generate confidence bands or prediction intervals around the fitted values? Once I get them, I'd like to add them to the plot. Example: library(nlme) library(lattice) Ortho - Orthodont Ortho$year - Ortho$year - 8 # make intercept = initial status Ortho.mix1 - lme(distance ~ year * Sex, data=Ortho, random = ~ 1 + year | Subject, method=ML, # correlation = corAR1 (form = ~ 1 | Subject) ) Ortho.mix1 # predicted values grid - expand.grid(year=0:6, Sex=c(Male, Female)) grid$age - grid$year+8 # plot vs. age fm.mix1 -cbind(grid, distance = predict(Ortho.mix1, newdata = grid, level=0)) xyplot(distance ~ age, data=fm.mix1, groups=Sex, type=b, pch=c(15,16), cex=1.2, auto.key=list(text=c(Male, Female), points = TRUE, x=8, y=26), main=Linear mixed model: predicted growth) Can someone help? -Michael Michael, the x,y location should be specified in the unit square (and you might want to set the 'corner' component). Ortho$year - Ortho$age - 8 ##fix typo xyplot(distance ~ age, data=fm.mix1, groups=Sex, type=b, pch=c(15,16), cex=1.2, auto.key=list(text=c(Male, Female), points = TRUE, x=0.1, y=0.8, corner=c(0,1))) See description of 'key' in ?xyplot. -Peter Ehlers -- Michael Friendly Email: friendly AT yorku DOT ca Professor, Psychology Dept. York University Voice: 416 736-5115 x66249 Fax: 416 736-5814 4700 Keele StreetWeb: http://www.datavis.ca Toronto, ONT M3J 1P3 CANADA __ 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] xyplot: key inside the plot region / lme: confidence bands for predicted
I have two questions related to plotting predicted values for a linear mixed model using xyplot: 1: With a groups= argument, I can't seem to get the key to appear inside the xyplot. (I have the Lattice book, but don't find an example that actually does this.) 2: With lme(), how can I generate confidence bands or prediction intervals around the fitted values? Once I get them, I'd like to add them to the plot. Example: library(nlme) library(lattice) Ortho - Orthodont Ortho$year - Ortho$year - 8 # make intercept = initial status Ortho.mix1 - lme(distance ~ year * Sex, data=Ortho, random = ~ 1 + year | Subject, method=ML, #correlation = corAR1 (form = ~ 1 | Subject) ) Ortho.mix1 # predicted values grid - expand.grid(year=0:6, Sex=c(Male, Female)) grid$age - grid$year+8 # plot vs. age fm.mix1 -cbind(grid, distance = predict(Ortho.mix1, newdata = grid, level=0)) xyplot(distance ~ age, data=fm.mix1, groups=Sex, type=b, pch=c(15,16), cex=1.2, auto.key=list(text=c(Male, Female), points = TRUE, x=8, y=26), main=Linear mixed model: predicted growth) Can someone help? -Michael -- Michael Friendly Email: friendly AT yorku DOT ca Professor, Psychology Dept. York University Voice: 416 736-5115 x66249 Fax: 416 736-5814 4700 Keele StreetWeb: http://www.datavis.ca Toronto, ONT M3J 1P3 CANADA __ 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] xyplot: key inside the plot region / lme: confidence bands for predicted
On 2010-07-02 9:37, Michael Friendly wrote: I have two questions related to plotting predicted values for a linear mixed model using xyplot: 1: With a groups= argument, I can't seem to get the key to appear inside the xyplot. (I have the Lattice book, but don't find an example that actually does this.) 2: With lme(), how can I generate confidence bands or prediction intervals around the fitted values? Once I get them, I'd like to add them to the plot. Example: library(nlme) library(lattice) Ortho - Orthodont Ortho$year - Ortho$year - 8 # make intercept = initial status Ortho.mix1 - lme(distance ~ year * Sex, data=Ortho, random = ~ 1 + year | Subject, method=ML, # correlation = corAR1 (form = ~ 1 | Subject) ) Ortho.mix1 # predicted values grid - expand.grid(year=0:6, Sex=c(Male, Female)) grid$age - grid$year+8 # plot vs. age fm.mix1 -cbind(grid, distance = predict(Ortho.mix1, newdata = grid, level=0)) xyplot(distance ~ age, data=fm.mix1, groups=Sex, type=b, pch=c(15,16), cex=1.2, auto.key=list(text=c(Male, Female), points = TRUE, x=8, y=26), main=Linear mixed model: predicted growth) Can someone help? -Michael Michael, the x,y location should be specified in the unit square (and you might want to set the 'corner' component). Ortho$year - Ortho$age - 8 ##fix typo xyplot(distance ~ age, data=fm.mix1, groups=Sex, type=b, pch=c(15,16), cex=1.2, auto.key=list(text=c(Male, Female), points = TRUE, x=0.1, y=0.8, corner=c(0,1))) See description of 'key' in ?xyplot. -Peter Ehlers __ 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.
