great minimal reproducible example, thanks. does something like this work?
#Log. Reg. model-all curric. concentrations including F1RTRCC as a predictor allCC <- svyglm(formula=F3ATTAINB~F1PARED+BYINCOME+F1RACE+F1SEX+F1RGPP2+F1HIMATH+F1RTRCC,family="binomial",design=elsq1ch_brr,subset=BYSCTRL==1&G10COHRT==1,na.action=na.exclude) summary(allCC) r <- residuals(allCC, type="response") f<-fitted(allCC) your_g<- cut(f, c(-Inf, quantile(f, (1:9)/10, Inf))) elsq1ch[ elsq1ch$BYSCTRL==1&elsq1ch$G10COHRT==1 , 'your_g' ] <- your_g elsq1ch[ elsq1ch$BYSCTRL==1&elsq1ch$G10COHRT==1 , 'r' ] <- r newdesign<-svrepdesign(variables = elsq1ch, repweights = elsq1ch[,18:217], weights = elsq1ch[,17], combined.weights = TRUE, type = "BRR") decilemodel<- svyglm(r~your_g, design=newdesign,subset=BYSCTRL==1&G10COHRT==1) regTermTest(decilemodel, ~your_g) On Wed, Nov 16, 2016 at 10:15 PM, Courtney Benjamin <cbenj...@btboces.org> wrote: > ?Hello R Experts, > > I am trying to implement the Archer-Lemeshow GOF Test for survey data on a > logistic regression model using the survey package based upon an R Help > Archive post that I found where Dr. Thomas Lumley advised how to do it: > http://r.789695.n4.nabble.com/Goodness-of-t-tests-for- > Complex-Survey-Logistic-Regression-td4668233.html > > Everything is going well until I get to the point where I have to add the > objects 'r' and 'g' as variables to the data frame by either using the > transform function or the update function to update the svrepdesign > object. The log. regression model involved uses a subset of data and some > of the values in the data frame are NA, so that is affecting my ability to > add 'r' and 'g' as variables; I am getting an error because I only have > 8397 rows for the new variables and 16197 in the data frame and svrepdesign > object. I am not sure how to overcome this error. > > The following is a MRE: > > ##Archer Lemeshow Goodness of Fit Test for Complex Survey Data with > Logistic Regression > > library(RCurl) > library(survey) > > data <- getURL("https://raw.githubusercontent.com/ > cbenjamin1821/careertech-ed/master/elsq1adj.csv") > elsq1ch <- read.csv(text = data) > > #Specifying the svyrepdesign object which applies the BRR weights > elsq1ch_brr<-svrepdesign(variables = elsq1ch[,1:16], repweights = > elsq1ch[,18:217], weights = elsq1ch[,17], combined.weights = TRUE, type = > "BRR") > elsq1ch_brr > > ##Resetting baseline levels for predictors > elsq1ch_brr <- update( elsq1ch_brr , F1HIMATH = relevel(F1HIMATH,"PreAlg > or Less") ) > elsq1ch_brr <- update( elsq1ch_brr , BYINCOME = relevel(BYINCOME,"0-25K") ) > elsq1ch_brr <- update( elsq1ch_brr , F1RACE = relevel(F1RACE,"White") ) > elsq1ch_brr <- update( elsq1ch_brr , F1SEX = relevel(F1SEX,"Male") ) > elsq1ch_brr <- update( elsq1ch_brr , F1RTRCC = relevel(F1RTRCC,"Academic") > ) > > #Log. Reg. model-all curric. concentrations including F1RTRCC as a > predictor > allCC <- svyglm(formula=F3ATTAINB~F1PARED+BYINCOME+F1RACE+F1SEX+ > F1RGPP2+F1HIMATH+F1RTRCC,family="binomial",design= > elsq1ch_brr,subset=BYSCTRL==1&G10COHRT==1,na.action=na.omit) > summary(allCC) > > #Recommendations from Lumley (from R Help Archive) on implementing the > Archer Lemeshow GOF test > r <- residuals(allCC, type="response") > f<-fitted(allCC) > g<- cut(f, c(-Inf, quantile(f, (1:9)/10, Inf))) > > # now create a new design object with r and g added as variables > #This is the area where I am having problems as my model involves a subset > and some values are NA as well > #I am also not sure if I am naming/specifying the new variables of r and g > properly > transform(elsq1ch,r=r,g=g) > elsq1ch_brr <- update(elsq1ch_brr,tag=g,tag=r) > #then: > decilemodel<- svyglm(r~g, design=newdesign) > regTermTest(decilemodel, ~g) > #is the F-adjusted mean residual test from the Archer Lemeshow paper > > Thank you, > Courtney > > ? > > Courtney Benjamin > > Broome-Tioga BOCES > > Automotive Technology II Teacher > > Located at Gault Toyota > > Doctoral Candidate-Educational Theory & Practice > > State University of New York at Binghamton > > cbenj...@btboces.org<mailto:cbenj...@btboces.org> > > 607-763-8633 > > [[alternative HTML version deleted]] > > ______________________________________________ > 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. > [[alternative HTML version deleted]] ______________________________________________ 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.
