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 [[alternative HTML version deleted]]
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 HaemFirst, 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
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 Jul 13, 2015, at 12:04 AM, Patty Haaem via R-help 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 HaemI would ask the question: where id you get the idea that there was an `na.include` function or option to `nmle`? I don't see it mentioned in the help page (and in fact see a specific warning about what will happen with dataset that have NA's. Most of the na.* options are actually functions that process the data and can be found with ?na.omit. I could certainly be uninformed about some new wonderful workaround to the problem, but at the moment I'm guessing you were hoping for a magical effect from na.include that doesn't yet have an underlying R incantation. -- David Winsemius Alameda, CA, USA