R help - Sep 2008 - Fw: Complex sampling survey _ Use of survey package

--------------------------------------------------
From: "Ahoussou Sylvie" <sylvie.ahoussou at antilles.inra.fr>
Sent: Friday, September 12, 2008 9:48 AM
To: "Thomas Lumley" <tlumley at u.washington.edu>
Subject: Re: [R] Complex sampling survey _ Use of survey package
> Thanks for your answer
>
> I think I made a mistake when I recopied the 5 first rows of my database
>
> here is the table with the comlums of interest
>
> num esp fpc1 Totanim Id_An
> 2045 G 551 12 10
> 2046 C 551 68 11
> 2070 G 551 9 50
> 2070 S 551 9 51
> 2070 S 551 9 52
>
>
>
> yes Totanim is the total number of animals in the farm and num is the 
> total number of herds
>
> I keep on obtaining this error message
>
> clustot<-svydesign(id=~num+ ~ Id_An, fpc=~fpc1+~Totanim, data=tab1)
>
> Erreur dans as.fpc(fpc, strata, ids) :
>  FPC implies >100% sampling in some strata.
>
>
> --------------------------------------------------
> From: "Thomas Lumley" <tlumley at u.washington.edu>
> Sent: Friday, September 12, 2008 12:02 AM
> To: "Ahoussou Sylvie" <sylvie.ahoussou at antilles.inra.fr>
> Cc: <r-help at r-project.org>
> Subject: Re: [R] Complex sampling survey _ Use of survey package
>
>> On Thu, 11 Sep 2008, Ahoussou Sylvie wrote:
>>
>>> Data base = tab1 here are the five first rows of the database (nrow
=
>>> 11792)
>>>
>>>
>>>
>>>
>>>     num
>>>     esp
>>>     Quarters
>>>     Totcat
>>>     Totshp
>>>     Totgt
>>>     Tbtpos
>>>     fpc1
>>>     Totanim
>>>     Id_An
>>>
>>>      10
>>>     2045
>>>     G
>>>     01-Q1
>>>     0
>>>     0
>>>     12
>>>     1
>>>     551
>>>     10
>>>     10
>>>
>>>      11
>>>     2046
>>>     G
>>>        01-Q1
>>>     8
>>>     0
>>>     60
>>>     1
>>>     551
>>>     11
>>>     11
>>>
>>>      50
>>>     2070
>>>     G
>>>        01-Q1
>>>     0
>>>     3
>>>     6
>>>     1
>>>     551
>>>     50
>>>     50
>>>
>>>      51
>>>     2070
>>>     S
>>>        01-Q1
>>>     0
>>>     3
>>>     6
>>>     1
>>>     551
>>>     51
>>>     51
>>>
>>>      52
>>>     2070
>>>     S
>>>     01-Q1
>>>     0
>>>     3
>>>     6
>>>     1
>>>     551
>>>     52
>>>     52
>>>
>>>
>>
>> This has 11 data values in each row but only 10 variable names.  If we 
>> assume the first number doesn't belong it, the fpc1 column lines up
>> correctly, so I will do that.
>>
>> It is surprising that Id_An is the same as Totanim for each of these
five
>> records
>>
>>>
>>> - First strata = herds
>>>
>>> herd's id column = num
>>>
>>> sampled in 551 herds (column fpc1)
>>>
>>>
>>>
>>> - Second strata = animals
>>>
>>> animal id column= Id_An
>>>
>>> sampled in Totanim
>>>
>>>
>>>
>>> I tried :
>>>
>>> clustot <- svydesign (id=~num+Id_An, fpc=~fpc1+~Totanim,
data=tab1)
>>>
>> This should be
>>   clustot <- svydesign (id=~num+Id_An, fpc=~fpc1+Totanim, data=tab1)
>> but that doesn't explain the problem
>>
>> Your svydesign() call looks correct if fpc1 is the total number of
herds
>> in the population and Totanim is the total number of animals in the 
>> particular herd. I am not sure from your explanation whether this is
how
>> the variables are defined.
>>
>>       -thomas
>>
>>
>>>
>>> and I get this error message
>>>
>>>
>>>
>>>> clustot <- svydesign(id=~num+Id_An, fpc=~fpc1+~Totanim,
data=tab1)
>>>
>>> Erreur dans as.fpc(fpc, strata, ids) :
>>>
>>>  FPC implies >100% sampling in some strata.
>>>
>>>
>>>
>>> I don't have any strata with 100% sampling so do you know which
>>> arguments of the fonction svydesign I'm supposed to use ?
>>>
>>>
>>>
>>> Thanks in advance
>>>
>>>
>>>
>>> AHOUSSOU Sylvie
>>> V?t?rinaire Epid?miologiste
>>> CIRAD Domaine Duclos
>>> 97 170 Petit-Bourg
>>> tel : 05 90 25 59 47
>>> [[alternative HTML version deleted]]
>>>
>>>
>>
>> Thomas Lumley Assoc. Professor, Biostatistics
>> tlumley at u.washington.edu University of Washington, Seattle
>>
>>
>>

Hi Tobias,

Thanks for your  answer but it doesn't change the error message

 clustot <- svydesign(id=~num+Id_An, fpc=~fpc1+Totanim, data=tab1)

Erreur dans as.fpc(fpc, strata, ids) :
  FPC implies >100% sampling in some strata

Maybe the probleme is that in some farms all the animals were examined (100% 
sampling) which is the case in my study sometimes


--------------------------------------------------
From: "Tobias Verbeke" <tobias.verbeke at gmail.com>
Sent: Friday, September 12, 2008 10:25 AM
To: "Ahoussou Sylvie" <sylvie.ahoussou at antilles.inra.fr>
Subject: Re: [R] Fw:  Complex sampling survey _ Use of survey package
> Hi Sylvie,
>
> You still use too much tilde signs (~) as Thomas Lumley already pointed 
> out.
>
> Replace your line
>
> clustot <- svydesign(id=~num+ ~ Id_An, fpc=~fpc1+~Totanim, data=tab1)
>
> with
>
> clustot <- svydesign(id=~num+Id_An, fpc=~fpc1+Totanim, data=tab1)
>
> Hope this helps,
> Tobias
>
> P.S.
>
> "~ num + Id_An" is called a formula in R and is omnipresent as
> an interface in R functions
>
>
> Ahoussou Sylvie wrote:
>>
>>
>> --------------------------------------------------
>> From: "Ahoussou Sylvie" <sylvie.ahoussou at
antilles.inra.fr>
>> Sent: Friday, September 12, 2008 9:48 AM
>> To: "Thomas Lumley" <tlumley at u.washington.edu>
>> Subject: Re: [R] Complex sampling survey _ Use of survey package
>>
>>> Thanks for your answer
>>>
>>> I think I made a mistake when I recopied the 5 first rows of my
database
>>>
>>> here is the table with the comlums of interest
>>>
>>> num esp fpc1 Totanim Id_An
>>> 2045 G 551 12 10
>>> 2046 C 551 68 11
>>> 2070 G 551 9 50
>>> 2070 S 551 9 51
>>> 2070 S 551 9 52
>>>
>>>
>>>
>>> yes Totanim is the total number of animals in the farm and num is
the
>>> total number of herds
>>>
>>> I keep on obtaining this error message
>>>
>>> clustot<-svydesign(id=~num+ ~ Id_An, fpc=~fpc1+~Totanim,
data=tab1)
>>>
>>> Erreur dans as.fpc(fpc, strata, ids) :
>>>  FPC implies >100% sampling in some strata.
>>>
>>>
>>> --------------------------------------------------
>>> From: "Thomas Lumley" <tlumley at u.washington.edu>
>>> Sent: Friday, September 12, 2008 12:02 AM
>>> To: "Ahoussou Sylvie" <sylvie.ahoussou at
antilles.inra.fr>
>>> Cc: <r-help at r-project.org>
>>> Subject: Re: [R] Complex sampling survey _ Use of survey package
>>>
>>>> On Thu, 11 Sep 2008, Ahoussou Sylvie wrote:
>>>>
>>>>> Data base = tab1 here are the five first rows of the
database (nrow =
>>>>> 11792)
>>>>>
>>>>>
>>>>>
>>>>>
>>>>>     num
>>>>>     esp
>>>>>     Quarters
>>>>>     Totcat
>>>>>     Totshp
>>>>>     Totgt
>>>>>     Tbtpos
>>>>>     fpc1
>>>>>     Totanim
>>>>>     Id_An
>>>>>
>>>>>      10
>>>>>     2045
>>>>>     G
>>>>>     01-Q1
>>>>>     0
>>>>>     0
>>>>>     12
>>>>>     1
>>>>>     551
>>>>>     10
>>>>>     10
>>>>>
>>>>>      11
>>>>>     2046
>>>>>     G
>>>>>        01-Q1
>>>>>     8
>>>>>     0
>>>>>     60
>>>>>     1
>>>>>     551
>>>>>     11
>>>>>     11
>>>>>
>>>>>      50
>>>>>     2070
>>>>>     G
>>>>>        01-Q1
>>>>>     0
>>>>>     3
>>>>>     6
>>>>>     1
>>>>>     551
>>>>>     50
>>>>>     50
>>>>>
>>>>>      51
>>>>>     2070
>>>>>     S
>>>>>        01-Q1
>>>>>     0
>>>>>     3
>>>>>     6
>>>>>     1
>>>>>     551
>>>>>     51
>>>>>     51
>>>>>
>>>>>      52
>>>>>     2070
>>>>>     S
>>>>>     01-Q1
>>>>>     0
>>>>>     3
>>>>>     6
>>>>>     1
>>>>>     551
>>>>>     52
>>>>>     52
>>>>>
>>>>>
>>>>
>>>> This has 11 data values in each row but only 10 variable names.
If we
>>>> assume the first number doesn't belong it, the fpc1 column
lines up
>>>> correctly, so I will do that.
>>>>
>>>> It is surprising that Id_An is the same as Totanim for each of
these
>>>> five records
>>>>
>>>>>
>>>>> - First strata = herds
>>>>>
>>>>> herd's id column = num
>>>>>
>>>>> sampled in 551 herds (column fpc1)
>>>>>
>>>>>
>>>>>
>>>>> - Second strata = animals
>>>>>
>>>>> animal id column= Id_An
>>>>>
>>>>> sampled in Totanim
>>>>>
>>>>>
>>>>>
>>>>> I tried :
>>>>>
>>>>> clustot <- svydesign (id=~num+Id_An, fpc=~fpc1+~Totanim,
data=tab1)
>>>>>
>>>> This should be
>>>>   clustot <- svydesign (id=~num+Id_An, fpc=~fpc1+Totanim,
data=tab1)
>>>> but that doesn't explain the problem
>>>>
>>>> Your svydesign() call looks correct if fpc1 is the total number
of
>>>> herds in the population and Totanim is the total number of
animals in
>>>> the particular herd. I am not sure from your explanation
whether this
>>>> is how the variables are defined.
>>>>
>>>>       -thomas
>>>>
>>>>
>>>>>
>>>>> and I get this error message
>>>>>
>>>>>
>>>>>
>>>>>> clustot <- svydesign(id=~num+Id_An,
fpc=~fpc1+~Totanim, data=tab1)
>>>>>
>>>>> Erreur dans as.fpc(fpc, strata, ids) :
>>>>>
>>>>>  FPC implies >100% sampling in some strata.
>>>>>
>>>>>
>>>>>
>>>>> I don't have any strata with 100% sampling so do you
know which
>>>>> arguments of the fonction svydesign I'm supposed to use
?
>>>>>
>>>>>
>>>>>
>>>>> Thanks in advance
>>>>>
>>>>>
>>>>>
>>>>> AHOUSSOU Sylvie
>>>>> V?t?rinaire Epid?miologiste
>>>>> CIRAD Domaine Duclos
>>>>> 97 170 Petit-Bourg
>>>>> tel : 05 90 25 59 47
>>>>> [[alternative HTML version deleted]]
>>>>>
>>>>>
>>>>
>>>> Thomas Lumley Assoc. Professor, Biostatistics
>>>> tlumley at u.washington.edu University of Washington, Seattle
>>>>
>>>>
>>>>
>>
>> ______________________________________________
>> R-help at r-project.org mailing list
>> 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 Fri, 12 Sep 2008, Ahoussou Sylvie wrote:
>
>
> --------------------------------------------------
> From: "Ahoussou Sylvie" <sylvie.ahoussou at
antilles.inra.fr>
> Sent: Friday, September 12, 2008 9:48 AM
> To: "Thomas Lumley" <tlumley at u.washington.edu>
> Subject: Re: [R] Complex sampling survey _ Use of survey package
>
>> Thanks for your answer
>> 
>> I think I made a mistake when I recopied the 5 first rows of my
database
>> 
>> here is the table with the comlums of interest
>> 
>> num esp fpc1 Totanim Id_An
>> 2045 G 551 12 10
>> 2046 C 551 68 11
>> 2070 G 551 9 50
>> 2070 S 551 9 51
>> 2070 S 551 9 52
>> 
>> yes Totanim is the total number of animals in the farm and num is the
total
>> number of herds
Do you mean 'fpc1 is the total number of herds'? That is what your 
svydesign() call says.
>> I keep on obtaining this error message
>> 
>> clustot<-svydesign(id=~num+ ~ Id_An, fpc=~fpc1+~Totanim, data=tab1)
>> 
>> Erreur dans as.fpc(fpc, strata, ids) :
>>  FPC implies >100% sampling in some strata.
Well, we seem to have either a bug or a problem with the data.

If you do
   options(error=recover)
before the svydesign() call you can go into as.fpc() and look at the data.

As an example;

Error in as.fpc(fpc, strata, ids) :
   FPC implies >100% sampling in some strata.

Enter a frame number, or 0 to exit

1: svydesign(id = ~dnum + snum, fpc = ~fpc1 + I(pmin(fpc2, 4)), data = 
apiclus2)
2: svydesign.default(id = ~dnum + snum, fpc = ~fpc1 + I(pmin(fpc2, 4)), 
data = apiclus2)
3: as.fpc(fpc, strata, ids)
Selection: 3
Called from: eval(expr, envir, enclos)
Browse[1]> which(sampsize>popsize, arr.ind=TRUE)
     row col
22   22   2
23   23   2
24   24   2
...

Browse[1]> sampsize[22,2]
[1] 5
Browse[1]> popsize[22,2]
[1] 4
Browse[1]> ids[22,]
    dnum    snum
22  200 200.841

So in this case one of the problems is in dnum 200, snum 841, where the 
population size was specified as 4 but the sample size is 5.

 	-thomas

Thomas Lumley			Assoc. Professor, Biostatistics
tlumley at u.washington.edu	University of Washington, Seattle