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, 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]]
Hi Thanks for code. see in line> -----Original Message----- > From: R-help [mailto:r-help-bounces at r-project.org] On Behalf Of li li > Sent: Tuesday, August 30, 2016 5:07 PM > To: r-help <r-help at 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 at 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 jak?koliv k n?mu p?ipojen? dokumenty jsou d?v?rn? a jsou ur?eny pouze jeho adres?t?m. Jestli?e jste obdr?el(a) tento e-mail omylem, informujte laskav? neprodlen? jeho odes?latele. Obsah tohoto emailu i s p??lohami a jeho kopie vyma?te ze sv?ho syst?mu. Nejste-li zam??len?m adres?tem tohoto emailu, nejste opr?vn?ni tento email jakkoliv u??vat, roz?i?ovat, kop?rovat ?i zve?ej?ovat. 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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.pikal at precheza.cz>:> Hi > > Thanks for code. > see in line > > > -----Original Message----- > > From: R-help [mailto:r-help-bounces at r-project.org] On Behalf Of li li > > Sent: Tuesday, August 30, 2016 5:07 PM > > To: r-help <r-help at 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 at 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 jak?koliv k n?mu p?ipojen? dokumenty jsou d?v?rn? a jsou > ur?eny pouze jeho adres?t?m. > Jestli?e jste obdr?el(a) tento e-mail omylem, informujte laskav? > neprodlen? jeho odes?latele. Obsah tohoto emailu i s p??lohami a jeho kopie > vyma?te ze sv?ho syst?mu. > Nejste-li zam??len?m adres?tem tohoto emailu, nejste opr?vn?ni tento email > jakkoliv u??vat, roz?i?ovat, kop?rovat ?i zve?ej?ovat. > Odes?latel e-mailu neodpov?d? za eventu?ln? ?kodu zp?sobenou modifikacemi > ?i zpo?d?n?m p?enosu e-mailu. > > V p??pad?, ?e je tento e-mail sou??st? obchodn?ho jedn?n?: > - vyhrazuje si odes?latel pr?vo ukon?it kdykoliv jedn?n? o uzav?en? > smlouvy, a to z jak?hokoliv d?vodu i bez uveden? d?vodu. > - a obsahuje-li nab?dku, je adres?t opr?vn?n nab?dku bezodkladn? p?ijmout; > Odes?latel tohoto e-mailu (nab?dky) vylu?uje p?ijet? nab?dky ze strany > p??jemce s dodatkem ?i odchylkou. > - trv? odes?latel na tom, ?e p??slu?n? smlouva je uzav?ena teprve > v?slovn?m dosa?en?m shody na v?ech jej?ch n?le?itostech. > - odes?latel tohoto emailu informuje, ?e nen? opr?vn?n uzav?rat za > spole?nost ??dn? smlouvy s v?jimkou p??pad?, kdy k tomu byl p?semn? zmocn?n > nebo p?semn? pov??en a takov? pov??en? nebo pln? moc byly adres?tovi tohoto > emailu p??padn? osob?, kterou adres?t zastupuje, p?edlo?eny nebo jejich > existence je adres?tovi ?i osob? j?m zastoupen? zn?m?. > > 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]]