Thanks Petr for the reply. When I run "plot(mod, type="all",log="x")", the tickmarks of the x axix include (0.02, 0.1, 1,10). But the log(Dose) should be less than 4. Anyway, I think there is something missing in the plot.drm function.
Hanna 2016-08-31 7:41 GMT-04:00 PIKAL Petr <petr.pi...@precheza.cz>: > Hi > > Thanks for code. > see in line > > > -----Original Message----- > > From: R-help [mailto:r-help-boun...@r-project.org] On Behalf Of li li > > Sent: Tuesday, August 30, 2016 5:07 PM > > To: r-help <r-help@r-project.org> > > Subject: [R] plot.drm in "drc" package > > > > Hi all, > > I am trying to use the drc package to fit 4L curve. > > I am so confused about the plot.drm function in the drc package. > > Particularly, I am confused about the scale of the xaxis in the plots > generated > > using the plot.drm function. See the example below: > > > > ## generate data and fit the model > > dose <- rep(50*2^(-(0:11)),3) > > dose > > d <- 100 > > c <- 1 > > b <- 1 > > e <- 1.6 > > y <- rnorm(length(dose))+ c+ (d-c)/(1+exp(b*(log(dose)-log(e)))) > > library(drc) > > mod <- drm(y~dose, fct = LL.4()) > > summary(mod) > > > > Now I plot the data and the fitted curve with the plot.drm using the code > > below and get the figure 1 below. > > > > > > ##obtaining figure 1 > > plot(mod, type="all",log="x") > > > > > > Next I plot the raw data and add the curve by extracting the estimate of > the > > parameters. > > > > ##extract parameters > > para <- mod$fit$par > > bhat<- para[1] > > chat <- para[2] > > dhat <- para[3] > > ehat <- para[4] > > > > ##plot figure 2 > > plot(log(dose),y) > > points(log(50*2^(-(0:11))), chat + > > (dhat-chat)/(1+exp(bhat*(log(50*2^(-(0:11)))-log(ehat)))), type="l") > > > > My question is regarding the figure 1 generated by the plot.drm. > > The x axis is the not the log scale of the doses. I checked the package > manual, > ^^^^^^^^^^^ > Well I am either missing something obvios but when I tried > > plot(mod, type="all",log="x") > > I got x axis with log scaling. Actually the result is the same as > > plot(mod, type="all") > > If you want x axis to be in original range you need to put empty string > > plot(mod, type="all",log="") > > Cheers > Petr > > > it says the default is log base 10. But it is not true in this case. > > Does some have some insight on the correct usage of the plot.drm > function. > > > > Thanks much in advance. > > Hanna > > > > [[alternative HTML version deleted]] > > > > ______________________________________________ > > 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. > > ________________________________ > Tento e-mail a jakékoliv k němu připojené dokumenty jsou důvěrné a jsou > určeny pouze jeho adresátům. > Jestliže jste obdržel(a) tento e-mail omylem, informujte laskavě > neprodleně jeho odesílatele. Obsah tohoto emailu i s přílohami a jeho kopie > vymažte ze svého systému. > Nejste-li zamýšleným adresátem tohoto emailu, nejste oprávněni tento email > jakkoliv užívat, rozšiřovat, kopírovat či zveřejňovat. > Odesílatel e-mailu neodpovídá za eventuální škodu způsobenou modifikacemi > či zpožděním přenosu e-mailu. > > V případě, že je tento e-mail součástí obchodního jednání: > - vyhrazuje si odesílatel právo ukončit kdykoliv jednání o uzavření > smlouvy, a to z jakéhokoliv důvodu i bez uvedení důvodu. > - a obsahuje-li nabídku, je adresát oprávněn nabídku bezodkladně přijmout; > Odesílatel tohoto e-mailu (nabídky) vylučuje přijetí nabídky ze strany > příjemce s dodatkem či odchylkou. > - trvá odesílatel na tom, že příslušná smlouva je uzavřena teprve > výslovným dosažením shody na všech jejích náležitostech. > - odesílatel tohoto emailu informuje, že není oprávněn uzavírat za > společnost žádné smlouvy s výjimkou případů, kdy k tomu byl písemně zmocněn > nebo písemně pověřen a takové pověření nebo plná moc byly adresátovi tohoto > emailu případně osobě, kterou adresát zastupuje, předloženy nebo jejich > existence je adresátovi či osobě jím zastoupené známá. > > This e-mail and any documents attached to it may be confidential and are > intended only for its intended recipients. > If you received this e-mail by mistake, please immediately inform its > sender. Delete the contents of this e-mail with all attachments and its > copies from your system. > If you are not the intended recipient of this e-mail, you are not > authorized to use, disseminate, copy or disclose this e-mail in any manner. > The sender of this e-mail shall not be liable for any possible damage > caused by modifications of the e-mail or by delay with transfer of the > email. > > In case that this e-mail forms part of business dealings: > - the sender reserves the right to end negotiations about entering into a > contract in any time, for any reason, and without stating any reasoning. > - if the e-mail contains an offer, the recipient is entitled to > immediately accept such offer; The sender of this e-mail (offer) excludes > any acceptance of the offer on the part of the recipient containing any > amendment or variation. > - the sender insists on that the respective contract is concluded only > upon an express mutual agreement on all its aspects. > - the sender of this e-mail informs that he/she is not authorized to enter > into any contracts on behalf of the company except for cases in which > he/she is expressly authorized to do so in writing, and such authorization > or power of attorney is submitted to the recipient or the person > represented by the recipient, or the existence of such authorization is > known to the recipient of the person represented by the recipient. > [[alternative HTML version deleted]] ______________________________________________ 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.