See section 8.4-8.5 of MASS 4th Ed. (the book) and the use of profile.nls() and friends for profiling the log likelihhood surface.
Warning: standard F,t approximations may be poor if the log likelihood is not nearly enough quadratic. The whole issue of what df to use is also contentious/unresolved. -- Bert Bert Gunter "Data is not information. Information is not knowledge. And knowledge is certainly not wisdom." -- Clifford Stoll On Tue, Nov 10, 2015 at 9:47 AM, David Winsemius <dwinsem...@comcast.net> wrote: > >> On Nov 9, 2015, at 7:19 AM, Catarina Silva >> <bolseiro.raiz.csi...@portucelsoporcel.com> wrote: >> >> I've tried others initial solutions and the adjustement was done to power >> model in ggplot - geom_smooth. >> But, with "nls" I can't do the confidence interval with ggplot - >> geom_smooth? I read that with "nls" we have to force "se=FALSE". Is this >> true? > > Well, sort of. Setting `se = FALSE` prevents the ggplot2 functions from > trying to force nls and nls.predict to do something that is not in their > design. > >> How can I draw confidence interval in the plot? >> >> I've done this: >>> ggplot(data,aes(x = idade,y = v_mt)) + >> + geom_point(alpha=2/10, shape=21,fill="darkgray", colour="black", size=3) >> + >> + geom_smooth(method = 'nls', formula = y ~ a * x^b, start = >> list(a=1,b=2),se=FALSE) >>> >> And then I don't have the confidence interval. >> >> If I do: >>> ggplot(data,aes(x = idade,y = v_mt)) + >> + geom_point(alpha=2/10, shape=21,fill="darkgray", colour="black", size=3) >> + >> + geom_smooth(method = 'nls', formula = y ~ a * x^b, start = list(a=1,b=2)) >> Error in pred$fit : $ operator is invalid for atomic vectors >>> >> >> Return error… >> > Read the help page for nls. The ‘se.fit' parameter is set to FALSE and > efforts to make it TRUE will be ignored. So `predict.nls` simply does not > return std-error estimates in the typical manner of other predict.* > functions. I believe this is because the authors of `nls` did not think there > was a clear answer to the question of what confidence bounds should be > returned. > > If you want to add confidence bounds to an nls, then you need to decide what > bounds to add, and then use the ggplot2 line-drawing functions to overlay > them on your own. I found posts in Rhelp that pointed me to the ‘nls2' > package, but when I tried to run the code I got messages saying that the > `as.lm` function could not be found. > > http://markmail.org/message/7kvolf5zzpqyb7l2?q=list:org%2Er-project%2Er-help+as%2Elm+is+a+linear+model+between+the+response+variable+and+the+gradient > >> require(nls2) > Loading required package: nls2 > Loading required package: proto >> fm <- nls(demand ~ SSasympOrig(Time, A, lrc), data = BOD) >> predict(as.lm(fm), interval = "confidence") > Error in predict(as.lm(fm), interval = "confidence") : > could not find function "as.lm" >> getAnywhere(as.lm) > no object named ‘as.lm’ was found > > > I also found a couple of posts on R-bloggers pointing me to the ‘propagate' > package which has two different methods for constructing confidence intervals. > > http://rmazing.wordpress.com/2013/08/14/predictnls-part-1-monte-carlo-simulation-confidence-intervals-for-nls-models/ > http://rmazing.wordpress.com/2013/08/26/predictnls-part-2-taylor-approximation-confidence-intervals-for-nls-models/ > > > > — > David. > >> Ty, >> Catarina Silva >> >> -----Original Message----- >> From: Jeff Newmiller [mailto:jdnew...@dcn.davis.ca.us] >> Sent: sábado, 7 de Novembro de 2015 01:09 >> To: bolseiro.raiz.csi...@portucelsoporcel.com; R mailling list >> Subject: Re: [R] [GGplot] Geom_smooth with formula "power"? >> >> Does [1] help? >> >> [1] >> http://stackoverflow.com/questions/10528631/add-exp-power-trend-line-to-a-ggplot >> --------------------------------------------------------------------------- >> Jeff Newmiller The ..... ..... Go Live... >> DCN:<jdnew...@dcn.davis.ca.us> Basics: ##.#. ##.#. Live Go... >> Live: OO#.. Dead: OO#.. Playing >> Research Engineer (Solar/Batteries O.O#. #.O#. with >> /Software/Embedded Controllers) .OO#. .OO#. rocks...1k >> --------------------------------------------------------------------------- >> Sent from my phone. Please excuse my brevity. >> >> On November 6, 2015 2:41:18 AM PST, Catarina Silva >> <bolseiro.raiz.csi...@portucelsoporcel.com> wrote: >>> Hi, >>> >>> It's possible to use ggplot and geom_smooth to adjust a power curve to >>> the data? >>> >>> Initially i have done the adjustement with nls and the formula 'a*x^b', >>> but resulted the singular matrix error for start solution. >>> Alternatively I used the log transformation and i had correct results, >>> but I can't draw a power curve on the graphic. >>> >>> Someone know how to solve this problem? >>> >>> > > David Winsemius > Alameda, CA, USA > > ______________________________________________ > R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see > 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 -- To UNSUBSCRIBE and more, see 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.