Hi all, I have a data set like this: Test.cox file: V1 V2 V3 Survival Event ann 13 WTHomo 4 1 ben 20 * 5 1 tom 40 Variant 6 1 where "*" indicates that I don't know what the value is for V3 for Ben. I've set up a Cox model to run like this: #!/usr/bin/Rscript library(bdsmatrix) library(kinship2) library(survival) library(coxme) death.dat <- read.table("Test.cox",header=T) deathdat.kmat <-2*with(death.dat,makekinship(famid,ID,faid,moid)) sink("Test.cox.R.Output") Model <- coxme(Surv(Survival,Event)~ strata(factor(V1)) + strata(factor(V2)) + factor(V3)) + (1|ID),data=death.dat,varlist=deathdat.kmat) Model sink() As you can see from the Test.cox file, I have a missing value "*". How and where do I tell the R script "treat * as a missing variable". If I can't incorporate missing values into the model, I assume the alternative is to remove all of the rows with missing data, which will greatly reduce my data set, as most rows have at least one missing variable. Thanks [[alternative HTML version deleted]]
First recode the * in NA: death.dat$v3[death.dat$v1==*] <- NA Include this in your model: na.rm=TRUE Or you could create a new dataset: newdata <- na.omit(death.dat) Shouro On Fri, Dec 19, 2014 at 11:12 AM, aoife doherty <aoife.m.doherty at gmail.com> wrote:> > Hi all, > > I have a data set like this: > > Test.cox file: > > V1 V2 V3 Survival Event > ann 13 WTHomo 4 1 > ben 20 * 5 1 > tom 40 Variant 6 1 > > > where "*" indicates that I don't know what the value is for V3 for Ben. > > I've set up a Cox model to run like this: > > #!/usr/bin/Rscript > library(bdsmatrix) > library(kinship2) > library(survival) > library(coxme) > death.dat <- read.table("Test.cox",header=T) > deathdat.kmat <-2*with(death.dat,makekinship(famid,ID,faid,moid)) > sink("Test.cox.R.Output") > Model <- coxme(Surv(Survival,Event)~ strata(factor(V1)) + > strata(factor(V2)) + factor(V3)) + > (1|ID),data=death.dat,varlist=deathdat.kmat) > Model > sink() > > > > As you can see from the Test.cox file, I have a missing value "*". How and > where do I tell the R script "treat * as a missing variable". If I can't > incorporate missing values into the model, I assume the alternative is to > remove all of the rows with missing data, which will greatly reduce my data > set, as most rows have at least one missing variable. > > Thanks > > [[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. >[[alternative HTML version deleted]]
Hi Aoife, I think that if you simply replace each "*" in the data file with "NA", then it should work ("NA" is usually interpreted as "missing" for those functions for which missingness is relevant). How you subsequently deal with records which have missing values is another question (or many questions ... ). So your data should look like: V1 V2 V3 Survival Event ann 13 WTHomo 4 1 ben 20 NA 5 1 tom 40 Variant 6 1 Hoping this helps, Ted. On 19-Dec-2014 10:12:00 aoife doherty wrote:> Hi all, > > I have a data set like this: > > Test.cox file: > > V1 V2 V3 Survival Event > ann 13 WTHomo 4 1 > ben 20 * 5 1 > tom 40 Variant 6 1 > > > where "*" indicates that I don't know what the value is for V3 for Ben. > > I've set up a Cox model to run like this: > >#!/usr/bin/Rscript > library(bdsmatrix) > library(kinship2) > library(survival) > library(coxme) > death.dat <- read.table("Test.cox",header=T) > deathdat.kmat <-2*with(death.dat,makekinship(famid,ID,faid,moid)) > sink("Test.cox.R.Output") > Model <- coxme(Surv(Survival,Event)~ strata(factor(V1)) + > strata(factor(V2)) + factor(V3)) + > (1|ID),data=death.dat,varlist=deathdat.kmat) > Model > sink() > > > > As you can see from the Test.cox file, I have a missing value "*". How and > where do I tell the R script "treat * as a missing variable". If I can't > incorporate missing values into the model, I assume the alternative is to > remove all of the rows with missing data, which will greatly reduce my data > set, as most rows have at least one missing variable. > > Thanks > > [[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.------------------------------------------------- E-Mail: (Ted Harding) <Ted.Harding at wlandres.net> Date: 19-Dec-2014 Time: 10:21:23 This message was sent by XFMail
Many thanks, I appreciate the response. When I convert the missing values to NA and run the cox model as described in previous post, the cox model seems to remove all of the rows with a missing value (as the number of rows "n" in the cox output after I completely remove any row with missing data is the same as the number of rows "n" in the cox output after I change the missing values to NA). What I had been hoping to do is not completely remove a row with missing data for a co-variable, but rather somehow censor or estimate a value for the missing value? In reality, I have ~600 people with survival data and say 6 variables attached to them. After I incorporate a 7th variable (for which the information isn't available for every individual), I have 400 people left. Since I still have survival data and almost all of the information for the other 200 people (the only thing missing is information about that 7th variable), it seems a waste to remove all of the survival data for 200 people over one co-variate. So I was hoping instead of completely removing the rows, to just somehow acknowledge that the data for this particular co-variate is missing in the model but not completely remove the row? This is more what I was hoping someone would know if it's possible to incorporate into the model I described above? Thanks On Fri, Dec 19, 2014 at 10:21 AM, Ted Harding <Ted.Harding at wlandres.net> wrote:> > Hi Aoife, > I think that if you simply replace each "*" in the data file > with "NA", then it should work ("NA" is usually interpreted > as "missing" for those functions for which missingness is > relevant). How you subsequently deal with records which have > missing values is another question (or many questions ... ). > > So your data should look like: > > V1 V2 V3 Survival Event > ann 13 WTHomo 4 1 > ben 20 NA 5 1 > tom 40 Variant 6 1 > > Hoping this helps, > Ted. > > On 19-Dec-2014 10:12:00 aoife doherty wrote: > > Hi all, > > > > I have a data set like this: > > > > Test.cox file: > > > > V1 V2 V3 Survival Event > > ann 13 WTHomo 4 1 > > ben 20 * 5 1 > > tom 40 Variant 6 1 > > > > > > where "*" indicates that I don't know what the value is for V3 for Ben. > > > > I've set up a Cox model to run like this: > > > >#!/usr/bin/Rscript > > library(bdsmatrix) > > library(kinship2) > > library(survival) > > library(coxme) > > death.dat <- read.table("Test.cox",header=T) > > deathdat.kmat <-2*with(death.dat,makekinship(famid,ID,faid,moid)) > > sink("Test.cox.R.Output") > > Model <- coxme(Surv(Survival,Event)~ strata(factor(V1)) + > > strata(factor(V2)) + factor(V3)) + > > (1|ID),data=death.dat,varlist=deathdat.kmat) > > Model > > sink() > > > > > > > > As you can see from the Test.cox file, I have a missing value "*". How > and > > where do I tell the R script "treat * as a missing variable". If I can't > > incorporate missing values into the model, I assume the alternative is to > > remove all of the rows with missing data, which will greatly reduce my > data > > set, as most rows have at least one missing variable. > > > > Thanks > > > > [[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. > > ------------------------------------------------- > E-Mail: (Ted Harding) <Ted.Harding at wlandres.net> > Date: 19-Dec-2014 Time: 10:21:23 > This message was sent by XFMail > ------------------------------------------------- >[[alternative HTML version deleted]]