No, Sarah. na.action must be a function, not a character string. But you're close: there is no na.include function, as the message says. It should be na.exclude . Cheers, Bert Bert Gunter "Data is not information. Information is not knowledge. And knowledge is certainly not wisdom." -- Clifford Stoll On Mon, Jul 13, 2015 at 7:35 AM, Sarah Goslee <sarah.goslee at gmail.com> wrote:> On Mon, Jul 13, 2015 at 3:04 AM, Patty Haaem via R-help > <r-help at r-project.org> wrote: >> Dear All,I am trying to fit one compartment IV bolus model on pharmacokinetic data using phenoModel function in nlme package, based on a tutorial entitled "Development of population PK model using R- Case study I". The codes are as fallowing: >> library(nlme)mydata.grp <- groupedData(CONC~TIME|CID,data=mydata)mydata.fit < -nlme(CONC~phenoModel(CID,TIME,AMT,lCl,lV),fixed=lCl+lV~1,random=pdDiag(lCl+lV~1), data=mydata.grp,start=c(-5,0),weight=varConstPower(const=1,fixed=list(power=1)),na.action=na.include,naPattern=~!is.na(CONC)) >> when I run above codes, I get the following error:Error in nlme.formula(CONC ~ phenoModel(CID, TIME, AMT, lCl, lV), fixed = lCl + : object 'na.include' not found >> could you please tell me, how should I correct the codes?Thanks in advanceElham Haem > > > First, you should not post in HTML. > > Second, you should put the argument in quotes: > > na.action="na.include" > > > Sarah > > >> >> >> [[alternative HTML version deleted]] >> > > -- > Sarah Goslee > http://www.functionaldiversity.org > > ______________________________________________ > 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.
On Mon, Jul 13, 2015 at 11:19 AM, Bert Gunter <bgunter.4567 at gmail.com> wrote:> No, Sarah. > > na.action must be a function, not a character string. But you're > close: there is no na.include function, as the message says. It > should be na.exclude .My apologies: I was assuming it worked like options():> class(options()$na.action)[1] "character"> options()$na.action[1] "na.omit" Sarah> > Cheers, > Bert > > > Bert Gunter > > "Data is not information. Information is not knowledge. And knowledge > is certainly not wisdom." > -- Clifford Stoll > > > On Mon, Jul 13, 2015 at 7:35 AM, Sarah Goslee <sarah.goslee at gmail.com> wrote: >> On Mon, Jul 13, 2015 at 3:04 AM, Patty Haaem via R-help >> <r-help at r-project.org> wrote: >>> Dear All,I am trying to fit one compartment IV bolus model on pharmacokinetic data using phenoModel function in nlme package, based on a tutorial entitled "Development of population PK model using R- Case study I". The codes are as fallowing: >>> library(nlme)mydata.grp <- groupedData(CONC~TIME|CID,data=mydata)mydata.fit < -nlme(CONC~phenoModel(CID,TIME,AMT,lCl,lV),fixed=lCl+lV~1,random=pdDiag(lCl+lV~1), data=mydata.grp,start=c(-5,0),weight=varConstPower(const=1,fixed=list(power=1)),na.action=na.include,naPattern=~!is.na(CONC)) >>> when I run above codes, I get the following error:Error in nlme.formula(CONC ~ phenoModel(CID, TIME, AMT, lCl, lV), fixed = lCl + : object 'na.include' not found >>> could you please tell me, how should I correct the codes?Thanks in advanceElham Haem >> >> >> First, you should not post in HTML. >> >> Second, you should put the argument in quotes: >> >> na.action="na.include" >> >> >> Sarah
On Jul 13, 2015, at 8:36 AM, Sarah Goslee wrote:> On Mon, Jul 13, 2015 at 11:19 AM, Bert Gunter <bgunter.4567 at gmail.com> wrote: >> No, Sarah. >> >> na.action must be a function, not a character string. But you're >> close: there is no na.include function, as the message says. It >> should be na.exclude . > > My apologies: I was assuming it worked like options(): > >> class(options()$na.action) > [1] "character" >> options()$na.action > [1] "na.omit"If such an option existed, then my understanding was that it would have an underlying function. But that's an inference from the various na.* functions that I find documented and vague memories of having seen code where there was a `get` or similar method of having a character value become a function name. I haven't actually tracked down the code for the substitution of function name for function value, since in the current instance it appears, looking first at `nlme.formula` and `model.frame.default`, that the character value gets sent to: External2(C_modelframe, ...) Best; David.> > Sarah > >> >> Cheers, >> Bert >> >> >> Bert Gunter >> >> "Data is not information. Information is not knowledge. And knowledge >> is certainly not wisdom." >> -- Clifford Stoll >> >> >> On Mon, Jul 13, 2015 at 7:35 AM, Sarah Goslee <sarah.goslee at gmail.com> wrote: >>> On Mon, Jul 13, 2015 at 3:04 AM, Patty Haaem via R-help >>> <r-help at r-project.org> wrote: >>>> Dear All,I am trying to fit one compartment IV bolus model on pharmacokinetic data using phenoModel function in nlme package, based on a tutorial entitled "Development of population PK model using R- Case study I". The codes are as fallowing: >>>> library(nlme)mydata.grp <- groupedData(CONC~TIME|CID,data=mydata)mydata.fit < -nlme(CONC~phenoModel(CID,TIME,AMT,lCl,lV),fixed=lCl+lV~1,random=pdDiag(lCl+lV~1), data=mydata.grp,start=c(-5,0),weight=varConstPower(const=1,fixed=list(power=1)),na.action=na.include,naPattern=~!is.na(CONC)) >>>> when I run above codes, I get the following error:Error in nlme.formula(CONC ~ phenoModel(CID, TIME, AMT, lCl, lV), fixed = lCl + : object 'na.include' not found >>>> could you please tell me, how should I correct the codes?Thanks in advanceElham Haem >>> >>> >>> First, you should not post in HTML. >>> >>> Second, you should put the argument in quotes: >>> >>> na.action="na.include" >>> >>> >>> Sarah > > ______________________________________________ > 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.David Winsemius Alameda, CA, USA