Hi

Thanks a lot, the corstr "exchangeable"does work. Didn't strike to me
for so long. Does the AIC value come out with the gee output?

By reference, I meant reference to a easy-read paper or web address
that can give me knowledge about implications of missing data.

Ta.

On 1/8/13, arun kirshna [via R]
<ml-node+s789695n4654902...@n4.nabble.com> wrote:
>
>
> HI,
> BP.stack5 is the one without missing values.
> na.omit(....).  Otherwise, I have to use the option na.action=.. in the
> ?geese() statement
>
> You need to read about the correlation structures.  IN unstructured option,
> more number of parameters needs to be estimated,  In repeated measures
> design, when the underlying structure is not known, it would be better to
> compare using different options (exchangeable is similar to compound
> symmetry) and select the one which provide the least value for AIC or BIC.
> Have a look at
>
> http://stats.stackexchange.com/questions/21771/how-to-perform-model-selection-in-gee-in-r
> It's not clear to me  "reference to write about missing values".
> A.K.
>
>
>
>
> ----- Original Message -----
> From: Usha Gurunathan <usha.nat...@gmail.com>
> To: arun <smartpink...@yahoo.com>
> Cc:
> Sent: Monday, January 7, 2013 6:12 PM
> Subject: Re: [R] random effects model
>
> Hi AK
>
> 2)I shall try putting exch. and check when I get home. Btw, what is
> BP.stack5? is it with missing values or only complete cases?
>
> I guess I am still not clear about the unstructured and exchangeable
> options, as in which one is better.
>
> 1)Rgding the summary(p): NA thing, I tried putting one of my gee equation.
>
> Can you suggest me a reference to write about" missing values and the
> implications for my results"
>
> Thanks.
>
>
>
> On 1/8/13, arun <smartpink...@yahoo.com> wrote:
>> HI,
>>
>> Just to add:
>> fit3<-geese(hibp~MaternalAge*time,id=CODEA,data=BP.stack5,family=binomial,corstr="exch",scale.fix=TRUE)
>> #works
>>  summary(fit3)$mean["p"]
>> #                             p
>> #(Intercept)         0.00000000
>> #MaternalAge4        0.49099242
>> #MaternalAge5        0.04686295
>> #time21              0.86164351
>> #MaternalAge4:time21 0.59258221
>> #MaternalAge5:time21 0.79909832
>>
>> fit4<-geese(hibp~MaternalAge*time,id=CODEA,data=BP.stack5,family=binomial,corstr="unstructured",scale.fix=TRUE)
>> #when the correlation structure is changed to "unstructured"
>> #Error in `contrasts<-`(`*tmp*`, value = contr.funs[1 + isOF[nn]]) :
>>  # contrasts can be applied only to factors with 2 or more levels
>> #In addition: Warning message:
>> #In is.na(rows) : is.na() applied to non-(list or vector) of type 'NULL'
>>
>>
>> Though, it works with data(Ohio)
>>
>> fit1<-geese(resp~age+smoke+age:smoke,id=id,data=ohio1,family=binomial,corstr="unstructured",scale.fix=TRUE)
>>  summary(fit1)$mean["p"]
>> #                      p
>> #(Intercept)  0.00000000
>> #age-1        0.60555454
>> #age0         0.45322698
>> #age1         0.01187725
>> #smoke1       0.86262269
>> #age-1:smoke1 0.17239050
>> #age0:smoke1  0.32223942
>> #age1:smoke1  0.36686706
>>
>>
>>
>> By checking:
>>  with(BP.stack5,table(MaternalAge,time))
>> #           time
>> #MaternalAge   14   21
>>   #        3 1104  864
>>    #       4  875  667
>>     #     5   67   53 #less number of observations
>>
>>
>>  BP.stack6 <- BP.stack5[order(BP.stack5$CODEA, BP.stack5$time),]
>>  head(BP.stack6)  # very few IDs with  MaternalAge==5
>> #       X CODEA Sex MaternalAge Education Birthplace AggScore IntScore
>> #1493 3.1     3   2           3         3          1        0        0
>> #3202 3.2     3   2           3         3          1        0        0
>> #1306 7.1     7   2           4         6          1        0        0
>> #3064 7.2     7   2           4         6          1        0        0
>> #1    8.1     8   2           4         4          1        0        0
>> #2047 8.2     8   2           4         4          1        0        0
>>  #         Categ time Obese Overweight hibp
>> #1493 Overweight   14     0          0    0
>> #3202 Overweight   21     0          1    0
>> #1306      Obese   14     0          0    0
>> #3064      Obese   21     1          1    0
>> #1        Normal   14     0          0    0
>> #2047     Normal   21     0          0    0
>> BP.stack7<-BP.stack6[BP.stack6$MaternalAge!=5,]
>>
>> BP.stack7$MaternalAge<-factor(as.numeric(as.character(BP.stack7$MaternalAge)
>>
>> fit5<-geese(hibp~MaternalAge*time,id=CODEA,data=BP.stack7,family=binomial,corstr="unstructured",scale.fix=TRUE)
>> #Error in `contrasts<-`(`*tmp*`, value = contr.funs[1 + isOF[nn]]) :
>>  # contrasts can be applied only to factors with 2 or more levels
>>
>>  with(BP.stack7,table(MaternalAge,time))  #It looks like the combinations
>> are still there
>> #           time
>> #MaternalAge   14   21
>>  #         3 1104  864
>>    #       4  875  667
>>
>> It works also with corstr="ar1".   Why do you gave the option
>> "unstructured"?
>> A.K.
>>
>>
>>
>>
>>
>>
>> ----- Original Message -----
>> From: rex2013 <usha.nat...@gmail.com>
>> To: r-help@r-project.org
>> Cc:
>> Sent: Monday, January 7, 2013 6:15 AM
>> Subject: Re: [R] random effects model
>>
>> Hi A.K
>>
>> Below is the comment I get, not sure why.
>>
>> BP.sub3 is the stacked data without the missing values.
>>
>> BP.geese3 <- geese(HiBP~time*MaternalAge,data=BP.sub3,id=CODEA,
>> family=binomial, corstr="unstructured", na.action=na.omit)Error in
>> `contrasts<-`(`*tmp*`, value = contr.funs[1 + isOF[nn]]) :
>>   contrasts can be applied only to factors with 2 or more levels
>>
>> Even though age has 3 levels; time has 14 years & 21 years; HIBP is a
>> binary response outcome.
>>
>> 2) When you mentioned summary(m1)$mean["p"] what did the p mean? i
>> used this in one of the gee command, it produced NA as answer?
>>
>> Many thanks
>>
>>
>>
>> On Mon, Jan 7, 2013 at 5:26 AM, arun kirshna [via R] <
>> ml-node+s789695n4654795...@n4.nabble.com> wrote:
>>
>>> Hi,
>>>
>>> I am  not very familiar with the geese/geeglm().  Is it from
>>> library(geepack)?
>>> Regarding your question:
>>> "
>>> Can you tell me if I can use the geese or geeglm function with this data
>>> eg: : HIBP~ time* Age
>>> Here age is a factor with 3 levels, time: 2 levels, HIBP = yes/no.
>>>
>>> From your original data:
>>> BP_2b<-read.csv("BP_2b.csv",sep="\t")
>>> head(BP_2b,2)
>>> #  CODEA Sex MaternalAge Education Birthplace AggScore IntScore Obese14
>>> #1     1  NA           3         4          1       NA       NA      NA
>>> #2     3   2           3         3          1        0        0       0
>>>  # Overweight14 Overweight21 Obese21 hibp14 hibp21
>>> #1           NA           NA      NA     NA     NA
>>> #2            0            1       0      0      0
>>>
>>> If I understand your new classification:
>>> BP.stacknormal<- subset(BP_2b,Obese14==0 & Overweight14==0 & Obese21==0
>>> &
>>> Overweight21==0)
>>> BP.stackObese <- subset(BP_2b,(Obese14==1& Overweight14==0 &
>>> Obese14==1&Overweight14==1)|(Obese14==1&Overweight14==1 & Obese21==1 &
>>> Overweight21==0)|(Obese14==1&Overweight14==0 & Obese21==0 &
>>> Overweight21==0)|(Obese14==0 & Overweight14==0 & Obese21==1 &
>>> Overweight21==0)|(Obese14==0 & Overweight14==0 & Obese21==1 &
>>> Overweight21==1)|(Obese14==0 & Overweight14==1 & Obese21==1
>>> &Overweight21==1)|(Obese14==1& Overweight14==1 & Obese21==1&
>>> Overweight21==1)) #check whether there are more classification that fits
>>> to
>>> #Obese
>>>  BP.stackOverweight <- subset(BP_2b,(Obese14==0 & Overweight14==1 &
>>> Obese21==0 & Overweight21==1)|(Obese14==0 &Overweight14==1 & Obese21==0
>>> &
>>> Overweight21==0)|(Obese14==0 & Overweight14==0 & Obese21==0 &
>>> Overweight21==1))
>>> BP.stacknormal$Categ<-"Normal"
>>> BP.stackObese$Categ<-"Obese"
>>> BP.stackOverweight$Categ <- "Overweight"
>>>
>>> BP.newObeseOverweightNormal<-na.omit(rbind(BP.stacknormal,BP.stackObese,BP.stackOverweight))
>>>
>>>  nrow(BP.newObeseOverweightNormal)
>>> #[1] 1581
>>> BP.stack3 <-
>>> reshape(BP.newObeseOverweightNormal,idvar="CODEA",timevar="time",sep="_",varying=list(c("Obese14","Obese21"),c("Overweight14","Overweight21"),c("hibp14","hibp21")),v.names=c("Obese","Overweight","hibp"),direction="long")
>>>
>>> library(car)
>>> BP.stack3$time<-recode(BP.stack3$time,"1=14;2=21")
>>> head(BP.stack3,2)
>>>   #  CODEA Sex MaternalAge Education Birthplace AggScore IntScore  Categ
>>> time
>>> #8.1     8   2           4         4          1        0        0 Normal
>>> 14
>>> #9.1     9   1           3         6          2        0        0 Normal
>>> 14
>>>   #  Obese Overweight hibp
>>> #8.1     0          0    0
>>>
>>> Now, your formula: (HIBP~time*Age), is it MaternalAge?
>>> If it is, it has three values
>>> unique(BP.stack3$MaternalAge)
>>> #[1] 4 3 5
>>> and for time (14,21) # If it says that geese/geeglm, contrasts could be
>>> applied with factors>=2 levels, what is the problem?
>>> If you take "Categ" variable, it also has 3 levels (Normal, Obese,
>>> Overweight).
>>>
>>>  BP.stack3$MaternalAge<-factor(BP.stack3$MaternalAge)
>>>  BP.stack3$time<-factor(BP.stack3$time)
>>>
>>> library(geepack)
>>> For your last question about how to get the p-values:
>>> # Using one of the example datasets:
>>> data(seizure)
>>>      seiz.l <- reshape(seizure,
>>>                        varying=list(c("base","y1", "y2", "y3", "y4")),
>>>                        v.names="y", times=0:4, direction="long")
>>>      seiz.l <- seiz.l[order(seiz.l$id, seiz.l$time),]
>>>      seiz.l$t <- ifelse(seiz.l$time == 0, 8, 2)
>>>      seiz.l$x <- ifelse(seiz.l$time == 0, 0, 1)
>>>      m1 <- geese(y ~ offset(log(t)) + x + trt + x:trt, id = id,
>>>                  data=seiz.l, corstr="exch", family=poisson)
>>>      summary(m1)
>>>
>>>  summary(m1)$mean["p"]
>>> #                    p
>>> #(Intercept) 0.0000000
>>> #x           0.3347040
>>> #trt         0.9011982
>>> #x:trt       0.6236769
>>>
>>>
>>> #If you need the p-values of the scale
>>>    summary(m1)$scale["p"]
>>>  #                   p
>>> #(Intercept) 0.0254634
>>>
>>> Hope it helps.
>>>
>>> A.K.
>>>
>>>
>>>
>>>
>>>
>>>
>>> ----- Original Message -----
>>> From: rex2013 <[hidden
>>> email]<http://user/SendEmail.jtp?type=node&node=4654795&i=0>>
>>>
>>> To: [hidden email]
>>> <http://user/SendEmail.jtp?type=node&node=4654795&i=1>
>>> Cc:
>>> Sent: Sunday, January 6, 2013 4:55 AM
>>> Subject: Re: [R] random effects model
>>>
>>> Hi A.K
>>>
>>> Regarding my question on comparing normal/ obese/overweight with blood
>>> pressure change, I did finally as per the first suggestion of stacking
>>> the
>>> data and creating a normal category . This only gives me a obese not
>>> obese
>>> 14, but when I did with the wide format hoping to  get  a
>>> obese14,normal14,overweight 14 Vs hibp 21, i could not complete any of
>>> the
>>> models.
>>> This time I classified obese=1 & overweight=1 as obese itself.
>>>
>>> Can you tell me if I can use the geese or geeglm function with this data
>>> eg: : HIBP~ time* Age
>>> Here age is a factor with 3 levels, time: 2 levels, HIBP = yes/no.
>>>
>>> It says geese/geeglm: contrast can be applied only with factor with 2 or
>>> more levels. What is the way to overcome this. Can I manipulate the data
>>> to
>>> make it work.
>>>
>>> I need to know if the demogrphic variables affect change in blood
>>> pressure
>>> status over time?
>>>
>>> How to get the p values with gee model?
>>>
>>> Thanks
>>> On Thu, Jan 3, 2013 at 5:06 AM, arun kirshna [via R] <
>>> [hidden email] <http://user/SendEmail.jtp?type=node&node=4654795&i=2>>
>>> wrote:
>>>
>>> > HI Rex,
>>> > If I take a small subset from your whole dataset, and go through your
>>> > codes:
>>> > BP_2b<-read.csv("BP_2b.csv",sep="\t")
>>> >  BP.sub<-BP_2b[410:418,c(1,8:11,13)] #deleted the columns that are not
>>> > needed
>>> >  BP.stacknormal<- subset(BP.subnew,Obese14==0 & Overweight14==0)
>>> > BP.stackObese <- subset(BP.subnew,Obese14==1)
>>> >  BP.stackOverweight <- subset(BP.subnew,Overweight14==1)
>>> > BP.stacknormal$Categ<-"Normal14"
>>> > BP.stackObese$Categ<-"Obese14"
>>> > BP.stackOverweight$Categ <- "Overweight14"
>>> >
>>> BP.newObeseOverweightNormal<-rbind(BP.stacknormal,BP.stackObese,BP.stackOverweight)
>>>
>>> >
>>> >  BP.newObeseOverweightNormal
>>> > #    CODEA Obese14 Overweight14 Overweight21 Obese21 hibp21
>>> > Categ
>>> > #411   541       0            0            0       0      0
>>> > Normal14
>>> > #415   545       0            0            1       1      1
>>> > Normal14
>>> > #418   549       0            0            1       0      0
>>> > Normal14
>>> > #413   543       1            0            1       1      0
>>> > Obese14
>>> > #417   548       0            1            1       0      0
>>> > Overweight14
>>> > BP.newObeseOverweightNormal$Categ<-
>>> > factor(BP.newObeseOverweightNormal$Categ)
>>> > BP.stack3 <-
>>> >
>>> reshape(BP.newObeseOverweightNormal,idvar="CODEA",timevar="time",sep="_",varying=list(c("Obese14","Obese21"),c("Overweight14","Overweight21")),v.names=c("Obese","Overweight"),direction="long")
>>>
>>> >
>>> > library(car)
>>> > BP.stack3$time<-recode(BP.stack3$time,"1=14;2=21")
>>> > BP.stack3 #Here Normal14 gets repeated even at time==21.  Given that
>>> > you
>>> > are using the "Categ" and "time" #columns in the analysis, it will
>>> > give
>>> > incorrect results.
>>> > #      CODEA hibp21        Categ time Obese Overweight
>>> > #541.1   541      0     Normal14   14     0          0
>>> > #545.1   545      1     Normal14   14     0          0
>>> > #549.1   549      0     Normal14   14     0          0
>>> > #543.1   543      0      Obese14   14     1          0
>>> > #548.1   548      0 Overweight14   14     0          1
>>> > #541.2   541      0     Normal14   21     0          0
>>> > #545.2   545      1     Normal14   21     1          1
>>> > #549.2   549      0     Normal14   21     0          1
>>> > #543.2   543      0      Obese14   21     1          1
>>> > #548.2   548      0 Overweight14   21     0          1
>>> > #Even if I correct the above codes, this will give incorrect
>>> > results/(error as you shown) because the response variable (hibp21)
>>> > gets
>>> > #repeated when you reshape it from wide to long.
>>> >
>>> > The correct classification might be:
>>> > BP_2b<-read.csv("BP_2b.csv",sep="\t")
>>> >  BP.sub<-BP_2b[410:418,c(1,8:11,13)]
>>> >
>>> BP.subnew<-reshape(BP.sub,idvar="CODEA",timevar="time",sep="",varying=list(c("Obese14","Obese21"),c("Overweight14","Overweight21")),v.names=c("Obese","Overweight"),direction="long")
>>>
>>> >
>>> > BP.subnew$time<-recode(BP.subnew$time,"1=14;2=21")
>>> >  BP.subnew<-na.omit(BP.subnew)
>>> >
>>> > BP.subnew$Categ[BP.subnew$Overweight==1 & BP.subnew$time==14 &
>>> > BP.subnew$Obese==0]<-"Overweight14"
>>> > BP.subnew$Categ[BP.subnew$Overweight==1 & BP.subnew$time==21 &
>>> > BP.subnew$Obese==0]<-"Overweight21"
>>> >  BP.subnew$Categ[BP.subnew$Obese==1 & BP.subnew$time==14 &
>>> > BP.subnew$Overweight==0]<-"Obese14"
>>> >  BP.subnew$Categ[BP.subnew$Obese==1 & BP.subnew$time==21 &
>>> > BP.subnew$Overweight==0]<-"Obese21"
>>> >  BP.subnew$Categ[BP.subnew$Overweight==1 & BP.subnew$time==21&
>>> > BP.subnew$Obese==1]<-"ObeseOverweight21"
>>> >  BP.subnew$Categ[BP.subnew$Overweight==1 & BP.subnew$time==14&
>>> > BP.subnew$Obese==1]<-"ObeseOverweight14"
>>> > BP.subnew$Categ[BP.subnew$Overweight==0 & BP.subnew$Obese==0
>>> > &BP.subnew$time==14]<-"Normal14"
>>> >  BP.subnew$Categ[BP.subnew$Overweight==0 & BP.subnew$Obese==0
>>> > &BP.subnew$time==21]<-"Normal21"
>>> >
>>> > BP.subnew$Categ<-factor(BP.subnew$Categ)
>>> > BP.subnew$time<-factor(BP.subnew$time)
>>> > BP.subnew
>>> > #      CODEA hibp21 time Obese Overweight             Categ
>>> > #541.1   541      0   14     0          0          Normal14
>>> > #543.1   543      0   14     1          0           Obese14
>>> > #545.1   545      1   14     0          0          Normal14
>>> > #548.1   548      0   14     0          1      Overweight14
>>> > #549.1   549      0   14     0          0          Normal14
>>> > #541.2   541      0   21     0          0          Normal21
>>> > #543.2   543      0   21     1          1 ObeseOverweight21
>>> > #545.2   545      1   21     1          1 ObeseOverweight21
>>> > #548.2   548      0   21     0          1      Overweight21
>>> > #549.2   549      0   21     0          1      Overweight21
>>> >
>>> > #NOw with the whole dataset:
>>> > BP.sub<-BP_2b[,c(1,8:11,13)] #change here and paste the above lines:
>>> >  head(BP.subnew)
>>> >     # CODEA hibp21 time Obese Overweight    Categ
>>> > #3.1      3      0   14     0          0 Normal14
>>> > #7.1      7      0   14     0          0 Normal14
>>> > #8.1      8      0   14     0          0 Normal14
>>> > #9.1      9      0   14     0          0 Normal14
>>> > #14.1    14      1   14     0          0 Normal14
>>> > #21.1    21      0   14     0          0 Normal14
>>> >
>>> > tail(BP.subnew)
>>> >   #     CODEA hibp21 time Obese Overweight             Categ
>>> > #8485.2  8485      0   21     1          1 ObeseOverweight21
>>> > #8506.2  8506      0   21     0          1      Overweight21
>>> > #8520.2  8520      0   21     0          0          Normal21
>>> > #8529.2  8529      1   21     1          1 ObeseOverweight21
>>> > #8550.2  8550      0   21     1          1 ObeseOverweight21
>>> > #8554.2  8554      0   21     0          0          Normal21
>>> >
>>> > summary(lme.1 <- lme(hibp21~time+Categ+ time*Categ,
>>> > data=BP.subnew,random=~1|CODEA, na.action=na.omit))
>>> > #Error in MEEM(object, conLin, control$niterEM) :
>>> >   #Singularity in backsolve at level 0, block 1
>>> > #May be because of the reasons I mentioned above.
>>> >
>>> > #YOu didn't mention the library(gee)
>>> > BP.gee8 <- gee(hibp21~time+Categ+time*Categ,
>>> > data=BP.subnew,id=CODEA,family=binomial,
>>> > corstr="exchangeable",na.action=na.omit)
>>> > #Beginning Cgee S-function, @(#) geeformula.q 4.13 98/01/27
>>> > #Error in gee(hibp21 ~ time + Categ + time * Categ, data = BP.subnew,
>>> > id
>>> =
>>> > CODEA,  :
>>> >   #rank-deficient model matrix
>>> > With your codes, it might have worked, but the results may be
>>> > inaccurate
>>> > # After running your whole codes:
>>> >  BP.gee8 <- gee(hibp21~time+Categ+time*Categ,
>>> > data=BP.stack3,id=CODEA,family=binomial,
>>> > corstr="exchangeable",na.action=na.omit)
>>> > #Beginning Cgee S-function, @(#) geeformula.q 4.13 98/01/27
>>> > #running glm to get initial regression estimate
>>> >    #        (Intercept)                   time           CategObese14
>>> >      #    -2.456607e+01           9.940875e-15           2.087584e-13
>>> >     # CategOverweight14      time:CategObese14 time:CategOverweight14
>>> >       #    2.087584e-13          -9.940875e-15          -9.940875e-15
>>> > #Error in gee(hibp21 ~ time + Categ + time * Categ, data = BP.stack3,
>>> > id
>>> =
>>> > CODEA,  :
>>> >  # Cgee: error: logistic model for probability has fitted value very
>>> close
>>> > to 1.
>>> > #estimates diverging; iteration terminated.
>>> >
>>> > In short, I think it would be better to go with the suggestion in my
>>> > previous email with adequate changes in "Categ" variable (adding
>>> > ObeseOverweight14, ObeseOverweight21 etc) as I showed here.
>>> >
>>> > A.K.
>>> >
>>> >
>>> >
>>> >
>>> >
>>> >
>>> >
>>> >
>>> > ------------------------------
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>>>
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