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#
# EXEMPLAR 2 - uncorrected data
# HOW TO USE THIS FILE
# A text version of this file (ex2.R) is also available which can just be sourced
# into the R program
# This file is intended for you to use interactively by pasting 
# the red bits into  R
# Comments are in black - red bits are commands that can be pasted 
# 
#
#########  ANY TEXT AFTER THE # CHARACTER ARE TREATED AS COMMENTS
#
# data stored in c:/GR/aprojects/peas/web/exemp2/data/.Rdata
# this file is c:/GR/aprojects/peas/web/exemp2/program_code/ex2_R.rtf
#
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#
#
library(survey)
#
#
shs.des_nc <- svydesign(id=~PSU, weights=~IND_WT,strata=~STRATUM,data=shs_nc)
#
# if you are smart at R you can use this code to work out which 
# PSUs are causing the problem
# First get unique combinations of PSU and stratum
# and then work out for which there are >1 startum

check1<-shs_nc[!duplicated(paste(shs_nc$PSU,shs_nc$STRATUM)),c(1,12)]
check2<-table(check1[,1])
check2[check2>1]
#
#  but you can force nesting
#
shs.des_nc <- svydesign(id=~PSU, weights=~IND_WT,strata=~STRATUM,data=shs_nc,nest=T)

svymean(~INTUSE,shs.des_nc,deff=T)
#
# this fails from a lonely PSU, need to try other options
options(survey.lonely.psu='removee')
svymean(~INTUSE,shs.des_nc,deff=T)
options(survey.lonely.psu='adjust')
svymean(~INTUSE,shs.des_nc,deff=T)
warnings()
#