[R] Archer-Lemeshow Goodness of Fit Test for Survey Data with Log. Regression

[Anthony Damico]

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 <cbenjami at 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
>
> cbenjami at btboces.org<mailto:cbenjami at btboces.org>
>
> 607-763-8633
>
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>
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