[R] plot.drm in "drc" package

[li li]

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 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]]