[R] svyglm
Hi,
I am trying to run analyzes incorporating sample weight, strata and cluster
(three-stage sample) with PNS data (national health survey) and is giving
error. I describe below the commands used. I could not make the code
reproducible properly.
Thanks,
#
library(survey)change to 0 and 1 variable
outcomedent2<-ifelse(consdentcat2==2,0,1)table(dent2)
dent2<-as.factor(dent2)str(dent2)reg<-cbind(reg, dent2)
#tchange to factor str(sexo)reg$sexo <- as.factor((reg$sexo))
#
pns2013design<-svydesign(id=~upa, nest=TRUE, strata = estrato, weight = peso,
data = reg)
PNS<-svyglm(dent2~sexo,design=pns2013design, method="logistic", data = reg)
Error in logistic(x = c(1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, :
unused arguments (x = c(1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1,
1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1,
1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1,
1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1,
1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1,
1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1,
1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1,
1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1,
1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1,
1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1,
1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1,
1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1,
1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1,
1,
###NOT running SVYGLM command#data for R-helpbteste <- reg[1:10, c(1, 4, 26,
27, 28)]#dput(bteste)###omitting most of the lines "9967.223281",
"9967.870849", "9968.207979", "997.0045537", "997.1451224", "997.1574275",
"997.1782368", "997.1812338", "997.2480231", "997.2531051", "997.3803145",
"997.4345619", "997.4363662", "997.5344599", "997.5964572", "997.7439813",
"997.8360773", "997.8770935", "997.8811374", "997.9147096",
"997.9563562", "9974.30392", "9974.344482", "9975.656981", "9977.382263",
"9979.999691", "998.0053953", "998.1069038", "998.2140192", "998.2655421",
"998.308316", "998.3090242", "998.3579509", "998.3656231", "998.3766007",
"998.6844831", "998.7030027", "998.7112321", "998.8021132", "998.8839799",
"998.9225688", "998.9270228", "998.9337225", "9983.555066",
"9985.353117", "9989.517638", "999.0713699", "999.0771916", "999.1021413",
"999.1779133", "999.2539765", "999.3435971", "999.3809978", "999.6348707",
"999.7597985", "999.8002746", "999.8819267", "999.8821907", "999.8921074",
"999.9211427", "9991.102816", "9991.440035", "9994.626337", "9994.723654",
"9996.637923", "9998.491819"), class = "factor")), .Names =
c("consdentcat2", "sexo", "estrato", "upa", "pesomorcc"), row.names = c(NA,
10L), class = "data.frame")##
bteste1 <-bteste[1:10, ]#bteste1 consdentcat2 sexo estrato upa
pesomorcc1 2 1 1110011 112 418.76819022 2 1
1110011 112 317.13175793 2 1 1110011 112 467.09452884
1 1 1110011 112 209.38409515 2 1 1110011 112
209.38409516 2 1 1110011 112 418.76819027 2 1
1110011 112 233.54726448 2 1 1110011 112 628.15228539
2 1 1110011 112 317.131757910 2 2 1110011 112
321.5014524>
_
Luciane Maria Pilotto
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Re: [R] clm funtion and CI
, 2015 at 7:43 PM, Luciane Maria Pilotto wrote: Hi, I'm working with ordinal logistic regression and fitting the model with the clm funtion of the ordinal package and would like to get the CI. According to the Tutorial on fitting Cumulative Link Models with the ordinal Package, Rune Haubo B Christensen (21 January 2015) you can run the OR, but not CI. The same happens with the clm2 for partial proportional odds. I appreciate any help !! Luciane __ R-help@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. -- Kevin Wright __ R-help@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.
[R] clm funtion and CI
Hi, I'm working with ordinal logistic regression and fitting the model with the clm funtion of the ordinal package and would like to get the CI. According to the Tutorial on fitting Cumulative Link Models with the ordinal Package, Rune Haubo B Christensen (21 January 2015) you can run the OR, but not CI. The same happens with the clm2 for partial proportional odds. I appreciate any help !! Luciane __ R-help@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.
Re: [R] help - hoslem.test
. ### load(id3.rda) attach(id3) #transformando q13 em binária (o/1) q131-ifelse(q13==1,0,ifelse(q13==2,1,ifelse(q13==3,1, ifelse(q13==4,1,ifelse(q13==5,1,NA) id3-cbind(id3,q131) id3$q131 - as.factor(id3$q131) str(id3) tp1 - glm(q131 ~ q11 + q10+q12+edcat + q08+q06+ q14, family = binomial(link = logit), data=id3, na.action=na.exclude) tp1 hoslem.test(tp1$q131, fitted(tp1), g=10) Em qui, 30/4/15, John Kane jrkrid...@inbox.com escreveu: Assunto: Re: [R] help - hoslem.test Para: PIKAL Petr petr.pi...@precheza.cz, Luciane Maria Pilotto r-help@r-project.org r-help@r- project.org Data: Quinta-feira, 30 de Abril de 2015, 11:51 Kevin Thorpe pointed out to me that there is a dropbox link at the very bottom of the post that I missed. :( I just downloaded it, read it in and it looks fine. John Kane Kingston ON Canada -Original Message- From: petr.pi...@precheza.cz Sent: Thu, 30 Apr 2015 14:25:23 + r-help@r-project.org Subject: Re: [R] help - hoslem.test Hi I agree with John Just small refinements in lines -Original Message- -Original Message- Sent: Thu, 30 Apr 2015 04:24:32 -0700 To: r-help@r-project.org, jrkrid...@inbox.com Subject: RE: [R] help - hoslem.test load(id3.rda) And what is this? We do not have access to your office or computer hard disc. Please read http://stackoverflow.com/questions/5963269/how-to-make-a- great-r-reproducible-example, see ?dput for sending data? It is very unlikely anyone here can help if we have no data. attach(id3) Do not use attach. It prevents from modifiyng id3. #transformando q13 em binária q131-ifelse(q13==1,1,ifelse(q13==2,2,ifelse(q13==3,2, ifelse(q13==4,2,ifelse(q13==5,2,NA) q131 - as.numeric(cut(q13, c(0,1.5,5))) x-1:7 x [1] 1 2 3 4 5 6 7 as.numeric(cut(x, c(0,1.5,5))) [1] 1 2 2 2 2 NA NA id3-cbind(id3,q131) rather dangerous in case id3 is not data.frame but matrix id3$q131 - as.factor(id3$q131) tp1 - glm(q131 ~ q11 + q10+q12+edcat + q08+q06+ q14, family = binomial(link = logit), data=id3) tp1 library(ResourceSelection) hoslem.test(tp1$q131, fitted(tp1), g=10) hoslem.test expects x to be a numeric vector of observations, binary (0/1). If I understand correctly tp1$q131 have values 1, 2 or NA. Cheers Petr dataframe: https://www.dropbox.com/s/9qrdf4mhd6tzypi/id3.rda?dl=0 __ Luciane Maria Pilotto Mestre e Doutoranda em Saúde Bucal Coletiva - FO/UFRGS NDE Odontologia - UNIVATES Telefone: (51) 84512344 Em qui, 30/4/15, John Kane jrkrid...@inbox.com escreveu: Assunto: RE: [R] help - hoslem.test Para: r-help@r-project.org Data: Quinta-feira, 30 de Abril de 2015, 7:52 http://stackoverflow.com/questions/5963269/how-to-make-a-great-r- reproducible-example John Kane Kingston ON Canada -Original Message- Sent: Wed, 29 Apr 2015 18:45:26 -0700 To: r-help@r-project.org Subject: [R] help - hoslem.test Hello, I'm working with ordinal logistic regression model (polr) and would like to test the proportional odds assumption. For this, I ran the binary logistic regressions with varying cutpoints on the dependent variable, as described in the following commands. When running the test of Hosmer and Lemeshow (hoslem.test) for residuals gives error. Thanks, Luciane __ R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
Re: [R] help - hoslem.test
load(id3.rda) attach(id3) #transformando q13 em binária q131-ifelse(q13==1,1,ifelse(q13==2,2,ifelse(q13==3,2, ifelse(q13==4,2,ifelse(q13==5,2,NA) id3-cbind(id3,q131) id3$q131 - as.factor(id3$q131) tp1 - glm(q131 ~ q11 + q10+q12+edcat + q08+q06+ q14, family = binomial(link = logit), data=id3) tp1 library(ResourceSelection) hoslem.test(tp1$q131, fitted(tp1), g=10) dataframe: https://www.dropbox.com/s/9qrdf4mhd6tzypi/id3.rda?dl=0 __ Luciane Maria Pilotto Mestre e Doutoranda em Saúde Bucal Coletiva - FO/UFRGS NDE Odontologia - UNIVATES Telefone: (51) 84512344 Em qui, 30/4/15, John Kane jrkrid...@inbox.com escreveu: Assunto: RE: [R] help - hoslem.test .org Data: Quinta-feira, 30 de Abril de 2015, 7:52 http://stackoverflow.com/questions/5963269/how-to-make-a-great-r-reproducible-example John Kane Kingston ON Canada -Original Message- Sent: Wed, 29 Apr 2015 18:45:26 -0700 To: r-help@r-project.org Subject: [R] help - hoslem.test Hello, I'm working with ordinal logistic regression model (polr) and would like to test the proportional odds assumption. For this, I ran the binary logistic regressions with varying cutpoints on the dependent variable, as described in the following commands. When running the test of Hosmer and Lemeshow (hoslem.test) for residuals gives error. Thanks, Luciane __ R-help@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. FREE ONLINE PHOTOSHARING - Share your photos [[elided Yahoo spam]] Visit http://www.inbox.com/photosharing to find out more! __ R-help@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.
[R] help - hoslem.test
Hello, I'm working with ordinal logistic regression model (polr) and would like to test the proportional odds assumption. For this, I ran the binary logistic regressions with varying cutpoints on the dependent variable, as described in the following commands. When running the test of Hosmer and Lemeshow (hoslem.test) for residuals gives error. Thanks, Luciane __ R-help@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.
