CRAN Package Check Results for Package survey

Last updated on 2026-10-24 17:51:45 CEST.

Flavor	Version	Tinstall	Tcheck	Ttotal	Status	Flags
r-devel-linux-x86_64-debian-clang	4.5	48.24	425.25	473.49	NOTE
r-devel-linux-x86_64-debian-gcc	4.5	36.55	279.85	316.40	ERROR
r-devel-linux-x86_64-fedora-clang	4.5	39.00	378.13	417.13	NOTE
r-devel-linux-x86_64-fedora-gcc	4.5	38.00	287.14	325.14	NOTE
r-devel-windows-x86_64	4.5	59.00	552.00	611.00	NOTE
r-patched-linux-x86_64	4.5	54.18	402.26	456.44	NOTE
r-release-linux-x86_64	4.5	51.38	400.00	451.38	NOTE
r-release-macos-arm64	4.5	11.00	100.00	111.00	OK
r-release-macos-x86_64	4.5	33.00	424.00	457.00	OK
r-release-windows-x86_64	4.5	63.00	454.00	517.00	NOTE
r-oldrel-macos-arm64	4.5	10.00	107.00	117.00	OK
r-oldrel-macos-x86_64	4.5	38.00	682.00	720.00	OK
r-oldrel-windows-x86_64	4.5	74.00	580.00	654.00	NOTE

Check Details

Version: 4.5
Check: R code for possible problems
Result: NOTE svycoxph.svyrep.design: no visible binding for global variable ‘parallel’ Undefined global functions or variables: parallel Flavors: r-devel-linux-x86_64-debian-clang, r-devel-linux-x86_64-debian-gcc, r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc, r-devel-windows-x86_64, r-patched-linux-x86_64, r-release-linux-x86_64, r-release-windows-x86_64, r-oldrel-windows-x86_64

Version: 4.5
Check: examples
Result: ERROR Running examples in ‘survey-Ex.R’ failed The error most likely occurred in: > base::assign(".ptime", proc.time(), pos = "CheckExEnv") > ### Name: anova.svyglm > ### Title: Model comparison for glms. > ### Aliases: anova.svyglm AIC.svyglm BIC.svyglm extractAIC.svyglm > ### extractAIC.svrepglm anova.svycoxph > ### Keywords: survey regression > > ### ** Examples > > data(api) > dclus2<-svydesign(id=~dnum+snum, weights=~pw, data=apiclus2) > > model0<-svyglm(I(sch.wide=="Yes")~ell+meals+mobility, design=dclus2, family=quasibinomial()) > model1<-svyglm(I(sch.wide=="Yes")~ell+meals+mobility+as.numeric(stype), + design=dclus2, family=quasibinomial()) > model2<-svyglm(I(sch.wide=="Yes")~ell+meals+mobility+stype, design=dclus2, family=quasibinomial()) > > anova(model2) Anova table: (Rao-Scott LRT) svyglm(formula = I(sch.wide == "Yes") ~ ell, design = dclus2, family = quasibinomial()) stats DEff df ddf p ell 1.1259 0.76870 1.00000 38 0.236339 meals 4.8189 1.24181 1.00000 37 0.058326 . mobility 0.3712 1.42335 1.00000 36 0.608418 stype 52.4054 2.43494 2.00000 34 0.001341 ** --- Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1 > anova(model0,model2) Working (Rao-Scott+F) LRT for stype in svyglm(formula = I(sch.wide == "Yes") ~ ell + meals + mobility + stype, design = dclus2, family = quasibinomial()) Working 2logLR = 21.52228 p= 0.0013407 (scale factors: 1.7 0.3 ); denominator df= 34 > anova(model1, model2) Working (Rao-Scott+F) LRT for stype - as.numeric(stype) in svyglm(formula = I(sch.wide == "Yes") ~ ell + meals + mobility + stype, design = dclus2, family = quasibinomial()) Working 2logLR = 25.10744 p= 1.816e-05 df=1; denominator df= 34 > > anova(model1, model2, method="Wald") Wald test for stype - as.numeric(stype) in svyglm(formula = I(sch.wide == "Yes") ~ ell + meals + mobility + stype, design = dclus2, family = quasibinomial()) F = 17.73552 on 1 and 34 df: p= 0.00017598 > > AIC(model0,model1, model2) eff.p AIC deltabar [1,] 3.538287 142.11041 1.179429 [2,] 6.248895 119.31208 1.562224 [3,] 7.202561 97.03351 1.440512 > BIC(model0, model2,maximal=model2) p BIC neff [1,] 4 120.8183 72.43313 [2,] 6 111.6461 NaN > > ## AIC for linear model is different because it considers the variance > ## parameter > > model0<-svyglm(api00~ell+meals+mobility, design=dclus2) > model1<-svyglm(api00~ell+meals+mobility+as.numeric(stype), + design=dclus2) > model2<-svyglm(api00~ell+meals+mobility+stype, design=dclus2) > modelnull<-svyglm(api00~1, design=dclus2) > > AIC(model0, model1, model2) eff.p AIC deltabar [1,] 8.471076 1511.490 2.117769 [2,] 8.930904 1493.666 1.786181 [3,] 9.161874 1458.431 1.526979 > > AIC(model0, model1, model2,modelnull, null_has_intercept=FALSE) eff.p AIC deltabar [1,] 14.810371 1524.169 2.962074 [2,] 15.317731 1506.439 2.552955 [3,] 14.119302 1468.346 2.017043 [4,] 8.973937 1614.039 4.486968 > > ## from ?twophase > data(nwtco) > dcchs<-twophase(id=list(~seqno,~seqno), strata=list(NULL,~rel), + subset=~I(in.subcohort | rel), data=nwtco) > a<-svycoxph(Surv(edrel,rel)~factor(stage)+factor(histol)+I(age/12), design=dcchs) Error in a$specials[[i]] : subscript out of bounds Calls: svycoxph ... model.matrix -> model.matrix.coxph -> delete.response -> off Execution halted Flavor: r-devel-linux-x86_64-debian-gcc

Version: 4.5
Check: tests
Result: ERROR Running ‘3stage2phase.R’ [2s/3s] Running ‘DBIcheck.R’ [2s/3s] Running ‘anova-svycoxph.R’ [2s/2s] Running ‘api.R’ [2s/2s] Running ‘badcal.R’ [2s/2s] Comparing ‘badcal.Rout’ to ‘badcal.Rout.save’ ... OK Running ‘brewer_cpp.R’ [2s/2s] Running ‘by_covmat_nodrop.R’ [2s/3s] Running ‘bycovmat.R’ [2s/2s] Running ‘caleg.R’ [3s/4s] Running ‘check.R’ [2s/2s] Comparing ‘check.Rout’ to ‘check.Rout.save’ ... OK Running ‘confintrep.R’ [2s/2s] Running ‘contrast-replicates.R’ [2s/2s] Running ‘coxph-termtest.R’ [2s/2s] Running ‘deff.R’ [2s/2s] Comparing ‘deff.Rout’ to ‘deff.Rout.save’ ... OK Running ‘defftest.R’ [2s/2s] Running ‘degf-subset.R’ [2s/2s] Running ‘degf-svrepdesign.R’ [2s/2s] Running ‘domain.R’ [2s/2s] Comparing ‘domain.Rout’ to ‘domain.Rout.save’ ... OK Running ‘fpc.R’ [2s/2s] Running ‘glm-scoping.R’ [2s/2s] Running ‘inf_cal_test.R’ [3s/4s] Running ‘kalton.R’ [2s/2s] Comparing ‘kalton.Rout’ to ‘kalton.Rout.save’ ... OK Running ‘logranktest.R’ [2s/2s] Running ‘lonely.psu.R’ [2s/3s] Comparing ‘lonely.psu.Rout’ to ‘lonely.psu.Rout.save’ ... OK Running ‘mf_frames2.R’ [2s/2s] Running ‘mf_subpop.R’ [2s/2s] Running ‘mtcars-var.R’ [2s/2s] Running ‘multiphase_simple.R’ [4s/5s] Running ‘multistage-rcpp.R’ [2s/3s] Running ‘multistage.R’ [2s/2s] Running ‘na_action.R’ [2s/2s] Running ‘na_weights.R’ [2s/2s] Running ‘newquantile.R’ [2s/2s] Running ‘nwts-cch.R’ [3s/3s] Running ‘nwts.R’ [4s/5s] Comparing ‘nwts.Rout’ to ‘nwts.Rout.save’ ... OK Running ‘poisson.R’ [2s/2s] Running ‘pps.R’ [2s/3s] Running ‘predict-NA.R’ [2s/3s] Running ‘qrule-swiss.R’ [2s/2s] Running ‘quantile.R’ [3s/3s] Comparing ‘quantile.Rout’ to ‘quantile.Rout.save’ ... OK Running ‘quantiles-chile.R’ [2s/2s] Running ‘rakecheck.R’ [2s/3s] Comparing ‘rakecheck.Rout’ to ‘rakecheck.Rout.save’ ... OK Running ‘raowuboot.R’ [2s/3s] Comparing ‘raowuboot.Rout’ to ‘raowuboot.Rout.save’ ... OK Running ‘regTermTest-missing.R’ [2s/3s] Running ‘regpredict.R’ [2s/3s] Comparing ‘regpredict.Rout’ to ‘regpredict.Rout.save’ ... OK Running ‘rss_scores.R’ [2s/2s] Running ‘scoping.R’ [2s/2s] Running ‘survcurve.R’ [2s/2s] Running ‘svyby-strings.R’ [2s/2s] Running ‘svyby_bug.R’ [2s/2s] Running ‘svyby_se.R’ [2s/2s] Running ‘svycontrast.R’ [2s/3s] Running ‘svyivreg-var.R’ [2s/2s] Running ‘svyivreg.R’ [2s/2s] Running ‘svyolr-rake-subset.R’ [2s/2s] Running ‘svyolr.R’ [2s/3s] Running ‘testthat.R’ [5s/6s] Running ‘toy_example_for_postStratify.R’ [2s/3s] Running ‘twophase.R’ [3s/3s] Running the tests in ‘tests/anova-svycoxph.R’ failed. Complete output: > > library(survey) Loading required package: grid Loading required package: Matrix Loading required package: survival Attaching package: 'survey' The following object is masked from 'package:graphics': dotchart > example(svycoxph, ask=FALSE) svycxp> ## Somewhat unrealistic example of nonresponse bias. svycxp> data(pbc, package="survival") svycxp> pbc$randomized<-with(pbc, !is.na(trt) & trt>0) svycxp> biasmodel<-glm(randomized~age*edema,data=pbc,family=binomial) svycxp> pbc$randprob<-fitted(biasmodel) svycxp> if (is.null(pbc$albumin)) pbc$albumin<-pbc$alb ##pre2.9.0 svycxp> dpbc<-svydesign(id=~1, prob=~randprob, strata=~edema, data=subset(pbc,randomized)) svycxp> rpbc<-as.svrepdesign(dpbc) svycxp> (model<-svycoxph(Surv(time,status>0)~log(bili)+protime+albumin,design=dpbc)) Error in a$specials[[i]] : subscript out of bounds Calls: example ... model.matrix -> model.matrix.coxph -> delete.response -> off Execution halted Running the tests in ‘tests/coxph-termtest.R’ failed. Complete output: > library(survey) Loading required package: grid Loading required package: Matrix Loading required package: survival Attaching package: 'survey' The following object is masked from 'package:graphics': dotchart > library(survival) > set.seed(2021-6-25) > test1 <- list(time=c(4,3,1,1,2,2,3), + status=c(1,1,1,0,1,1,0), + x1=as.factor(rbinom(7, 2, 0.5)), + x=c(0,2,1,1,1,0,0)) > # Fit a stratified model > mod_c <- coxph(Surv(time, status) ~ x1 + x, test1) > mod_d <- coxph(Surv(time, status) ~ x + x1, test1) > stopifnot(all.equal(regTermTest(mod_c, ~x1, df = Inf)[c("chisq","df","test.terms","p")], + regTermTest(mod_d, ~x1, df = Inf)[c("chisq","df","test.terms","p")])) Error in (function (cond) : error in evaluating the argument 'target' in selecting a method for function 'all.equal': subscript out of bounds Calls: stopifnot ... model.matrix.coxph -> delete.response -> off -> <Anonymous> Execution halted Running the tests in ‘tests/logranktest.R’ failed. Complete output: > ## StackOverflow 63333282 > > library(survey) Loading required package: grid Loading required package: Matrix Loading required package: survival Attaching package: 'survey' The following object is masked from 'package:graphics': dotchart > D = data.frame(unique_id = 1:135, + + weights = rep(1,135), + + event_time = c(0.53512437, 1.35655869, 2.00414189, 2.37276648, 3.20343526, 0.96618494, 2.57894309, 0.94575080, 1.25347833, 1.44416450, 5.04038200, 7.80587169 , + + 6.53631154, 6.31914568, 7.00146597, 9.67616088, 7.94212358, 9.70693890, 10.67575835, 10.06764688, 12.29175616, 13.60092871, 13.12508566, 14.66417522, + + 15.35250691, 0.93368707, 0.19087611, 3.15533767, 4.40821633, 17.54334957, 17.95177642, 15.50903946, 16.48376185, 20.87956697, 21.24571398, 22.34297263, + + 23.36042629, 21.01760215, 23.84785038, 26.06105822, 4.16866350, 1.96922485, 0.66199008, 6.76987830, 1.55617685, 0.19095871, 3.13291784, 5.43159409, + + 9.55805671, 4.31437322, 0.78259860, 5.26415156, 3.45095686, 1.69128712, 8.41942426, 3.33748695, 6.08516173, 2.72897404, 0.22789783, 0.86348009, + + 2.35707587, 2.97477615, 12.33273800, 0.58532123, 0.14586238, 10.67948547, 4.07655972, 3.94405136, 0.37226898, 1.42558725, 1.47680658, 4.22506540, + + 1.56703478, 8.37484756, 12.54015087, 1.80994787, 3.66453633, 1.02834532, 1.99065652, 1.23577436, 16.21981618, 14.35039798, 4.15321606, 2.79740679, + + 0.35538726, 7.46823358, 1.66329088, 7.46525382, 2.62734831, 3.19057957, 0.33317193, 0.09122886, 9.14616245, 2.48542578, 2.37569263, 5.48499630, + + 2.22749399, 2.64816296, 0.97101545, 1.42468625, 1.27668904, 0.03692447, 1.98783210, 5.47692729, 3.88316178, 0.32921277, 1.77225345, 9.33268901, + + 2.44517775, 1.49813702, 2.56059172, 3.43194832, 1.22955630, 3.56263947, 9.07060099, 3.58312362, 2.22755370, 4.24783776, 3.46364804, 1.61671354, + + 11.10973565, 7.18764270, 1.80400046, 6.39833474, 6.72825192, 6.46063344, 5.76855531, 5.27157807, 4.66154734, 3.50019718, 2.27156678, 3.28531594, + + 2.35699896, 2.94956000, 8.85381736), + + event_flag = 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, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 0, 1, 1, 1, 0, 0, 0, 1, + + 1, 0, 0, 0, 0, 1, 0, 0, 1, 1, 1, 1, 1, 0, 0, 1, 0, 0, 0, 0, 0, 1, 1, 1, 0, 0, 0, 0, 0, 0, 0, 1, 1, 1, 1, 0, 1, 1, 1, 1, 0, 1, 0, 0, 1, 0, 0, 1, 0, 1, 1, 1, + + 1, 1, 1, 0, 1, 0, 1, 0, 1, 1, 0, 1, 1, 1, 0, 0, 0, 0, 0, 0, 1, 0, 0, 0, 1, 0, 1, 1, 0, 0, 0), + + group = c(rep("group1", 40), rep("group2", 95))) > > > > svykm_formula = as.formula("Surv(event_time, event_flag) ~ group") > > svy_design = svydesign( ids = ~unique_id , weights = ~weights, data = D ) > > a<-svylogrank(formula = svykm_formula, design = svy_design) Error in a$specials[[i]] : subscript out of bounds Calls: svylogrank ... model.matrix -> model.matrix.coxph -> delete.response -> off Execution halted Running the tests in ‘tests/nwts-cch.R’ failed. Complete output: > library(survey) Loading required package: grid Loading required package: Matrix Loading required package: survival Attaching package: 'survey' The following object is masked from 'package:graphics': dotchart > library(survival) > data(nwtco) > > ntwco<-subset(nwtco, !is.na(edrel)) > > load("nwtco-subcohort.rda") > nwtco$subcohort<-subcohort > > d_BorganII <- twophase(id=list(~seqno,~seqno), + strata=list(NULL,~interaction(instit,rel)), + data=nwtco, subset=~I(rel |subcohort)) > > ##Coefficient results same as Splus with code from > ## http://faculty.washington.edu/norm/software.html > ## SE slightly larger due to using sandwich variance. > > svycoxph(Surv(edrel, rel)~factor(stage)+factor(histol)+I(age/12), design=d_BorganII) Error in a$specials[[i]] : subscript out of bounds Calls: svycoxph ... model.matrix -> model.matrix.coxph -> delete.response -> off Execution halted Running the tests in ‘tests/scoping.R’ failed. Complete output: > > ## regression test for testing regression > > library(survey) Loading required package: grid Loading required package: Matrix Loading required package: survival Attaching package: 'survey' The following object is masked from 'package:graphics': dotchart > data(api) > > dstrat<-svydesign(id=~1,strata=~stype, weights=~pw, data=apistrat, fpc=~fpc) > > > f<-function(){ + form<-acs.46~stype + svyglm(formula=form, design = dstrat) + } > > g<-function(form){ + svyglm(formula=form, design = dstrat) + } > f() Stratified Independent Sampling design svydesign(id = ~1, strata = ~stype, weights = ~pw, data = apistrat, fpc = ~fpc) Call: svyglm(formula = form, design = dstrat) Coefficients: (Intercept) stypeH stypeM 28.7449 0.7551 0.4022 Degrees of Freedom: 133 Total (i.e. Null); 129 Residual (66 observations deleted due to missingness) Null Deviance: 1838 Residual Deviance: 1835 AIC: NA > g(acs.46~stype) Stratified Independent Sampling design svydesign(id = ~1, strata = ~stype, weights = ~pw, data = apistrat, fpc = ~fpc) Call: svyglm(formula = form, design = dstrat) Coefficients: (Intercept) stypeH stypeM 28.7449 0.7551 0.4022 Degrees of Freedom: 133 Total (i.e. Null); 129 Residual (66 observations deleted due to missingness) Null Deviance: 1838 Residual Deviance: 1835 AIC: NA > > f<-function(){ + form<-Surv(acs.46)~stype + svycoxph(formula=form, design = dstrat) + } > > g<-function(form){ + svycoxph(formula=form, design = dstrat) + } > > f() Error in a$specials[[i]] : subscript out of bounds Calls: f ... model.matrix -> model.matrix.coxph -> delete.response -> off Execution halted Running the tests in ‘tests/survcurve.R’ failed. Complete output: > library(survey) Loading required package: grid Loading required package: Matrix Loading required package: survival Attaching package: 'survey' The following object is masked from 'package:graphics': dotchart > library(survival) > > pbc2<-rbind(pbc,pbc) > pbc2$id<-rep(1:418,2) > > dpbc1<-svydesign(id=~1, data=pbc) Warning message: In svydesign.default(id = ~1, data = pbc) : No weights or probabilities supplied, assuming equal probability > dpbc2<-svydesign(id=~id, data=pbc2) Warning message: In svydesign.default(id = ~id, data = pbc2) : No weights or probabilities supplied, assuming equal probability > > s1<-svykm(Surv(time,status>0)~1, subset(dpbc1, bili>6), se=TRUE) > s2<-svykm(Surv(time,status>0)~1, subset(dpbc2, bili>6), se=TRUE) > > (c1<-confint(s1,(1:5)*365)) 0.025 0.975 365 0.6446215 0.8594153 730 0.5410938 0.7766848 1095 0.2683127 0.5103356 1460 0.1444731 0.3722001 1825 0.1009672 0.3204713 > (c2<-confint(s2,(1:5)*365)) 0.025 0.975 365 0.6446215 0.8594153 730 0.5410938 0.7766848 1095 0.2683127 0.5103356 1460 0.1444731 0.3722001 1825 0.1009672 0.3204713 > all.equal(c1, c2) [1] TRUE > > m1<-svycoxph(Surv(time,status>0)~log(bili), design=dpbc1) Error in a$specials[[i]] : subscript out of bounds Calls: svycoxph ... model.matrix -> model.matrix.coxph -> delete.response -> off Execution halted Running the tests in ‘tests/twophase.R’ failed. Complete output: > library(survey) Loading required package: grid Loading required package: Matrix Loading required package: survival Attaching package: 'survey' The following object is masked from 'package:graphics': dotchart > > ## two-phase simple random sampling. > data(pbc, package="survival") > pbc$id<-1:nrow(pbc) > pbc$randomized<-with(pbc, !is.na(trt) & trt>-9) > (d2pbc<-twophase(id=list(~id,~id), data=pbc, subset=~I(!randomized))) Two-phase sparse-matrix design: twophase(id = list(~id, ~id), data = pbc, subset = ~I(!randomized)) Phase 1: Independent Sampling design (with replacement) svydesign(ids = ~id) Phase 2: Independent Sampling design svydesign(ids = ~id, fpc = `*phase1*`) > m<-svymean(~bili, d2pbc) > all.equal(as.vector(coef(m)),with(pbc, mean(bili[!randomized]))) [1] TRUE > all.equal(as.vector(SE(m)), + with(pbc, sd(bili[!randomized])/sqrt(sum(!randomized))), + tolerance=0.002) [1] TRUE > > ## two-stage sampling as two-phase > data(mu284) > ii<-with(mu284, c(1:15, rep(1:5,n2[1:5]-3))) > mu284.1<-mu284[ii,] > mu284.1$id<-1:nrow(mu284.1) > mu284.1$sub<-rep(c(TRUE,FALSE),c(15,34-15)) > dmu284<-svydesign(id=~id1+id2,fpc=~n1+n2, data=mu284) > ## first phase cluster sample, second phase stratified within cluster > (d2mu284<-twophase(id=list(~id1,~id),strata=list(NULL,~id1), + fpc=list(~n1,NULL),data=mu284.1,subset=~sub,method="approx")) Two-phase design: twophase(id = list(~id1, ~id), strata = list(NULL, ~id1), fpc = list(~n1, NULL), data = mu284.1, subset = ~sub, method = "approx") Phase 1: 1 - level Cluster Sampling design With (5) clusters. svydesign(ids = ~id1, fpc = ~n1) Phase 2: Stratified Independent Sampling design svydesign(ids = ~id, strata = ~id1, fpc = `*phase1*`) > (d22mu284<-twophase(id=list(~id1,~id),strata=list(NULL,~id1), + fpc=list(~n1,NULL),data=mu284.1,subset=~sub,method="full")) Two-phase sparse-matrix design: twophase(id = list(~id1, ~id), strata = list(NULL, ~id1), fpc = list(~n1, NULL), data = mu284.1, subset = ~sub, method = "full") Phase 1: 1 - level Cluster Sampling design With (5) clusters. svydesign(ids = ~id1, fpc = ~n1) Phase 2: Stratified Independent Sampling design svydesign(ids = ~id, strata = ~id1, fpc = `*phase1*`) > summary(d2mu284) Two-phase design: twophase(id = list(~id1, ~id), strata = list(NULL, ~id1), fpc = list(~n1, NULL), data = mu284.1, subset = ~sub, method = "approx") Phase 1: 1 - level Cluster Sampling design With (5) clusters. svydesign(ids = ~id1, fpc = ~n1) Probabilities: Min. 1st Qu. Median Mean 3rd Qu. Max. 0.1 0.1 0.1 0.1 0.1 0.1 Population size (PSUs): 50 Phase 2: Stratified Independent Sampling design svydesign(ids = ~id, strata = ~id1, fpc = `*phase1*`) Probabilities: Min. 1st Qu. Median Mean 3rd Qu. Max. 0.3333 0.3750 0.4286 0.4674 0.6000 0.6000 Stratum Sizes: 19 31 45 47 50 obs 3 3 3 3 3 design.PSU 3 3 3 3 3 actual.PSU 3 3 3 3 3 Population stratum sizes (PSUs): 19 31 45 47 50 5 7 8 5 9 Data variables: [1] "id1" "n1" "id2" "y1" "n2" "id" "sub" > t1<-svytotal(~y1, dmu284) > t2<-svytotal(~y1, d2mu284) > t22<-svytotal(~y1,d22mu284) > m1<-svymean(~y1, dmu284) > m2<-svymean(~y1, d2mu284) > m22<-svymean(~y1, d22mu284) > all.equal(coef(t1),coef(t2)) [1] TRUE > all.equal(coef(t1),coef(t22)) [1] TRUE > all.equal(coef(m1),coef(m2)) [1] TRUE > all.equal(coef(m1),coef(m22)) [1] TRUE > all.equal(as.vector(SE(m1)),as.vector(SE(m2))) [1] TRUE > all.equal(as.vector(SE(m1)),as.vector(SE(m22))) [1] TRUE > all.equal(as.vector(SE(t1)),as.vector(SE(t2))) [1] TRUE > all.equal(as.vector(SE(t1)),as.vector(SE(t22))) [1] TRUE > > ## case-cohort design > ##this example requires R 2.3.1 or later for cch and data. > library("survival") > data(nwtco, package="survival") > ## unstratified, equivalent to Lin & Ying (1993) > print(dcchs<-twophase(id=list(~seqno,~seqno), strata=list(NULL,~rel), + subset=~I(in.subcohort | rel), data=nwtco)) Two-phase sparse-matrix design: twophase(id = list(~seqno, ~seqno), strata = list(NULL, ~rel), subset = ~I(in.subcohort | rel), data = nwtco) Phase 1: Independent Sampling design (with replacement) svydesign(ids = ~seqno) Phase 2: Stratified Independent Sampling design svydesign(ids = ~seqno, strata = ~rel, fpc = `*phase1*`) > cch1<-svycoxph(Surv(edrel,rel)~factor(stage)+factor(histol)+I(age/12), + design=dcchs) Error in a$specials[[i]] : subscript out of bounds Calls: svycoxph ... model.matrix -> model.matrix.coxph -> delete.response -> off Execution halted Flavor: r-devel-linux-x86_64-debian-gcc

Version: 4.5
Check: re-building of vignette outputs
Result: ERROR Error(s) in re-building vignettes: ... --- re-building ‘survey-sae.html.asis’ using asis --- finished re-building ‘survey-sae.html.asis’ --- re-building ‘multiphase.Rmd’ using rmarkdown [WARNING] Deprecated: --mathjax. Use --math-method=mathjax[:URL] instead. --- finished re-building ‘multiphase.Rmd’ --- re-building ‘domain.Rnw’ using Sweave Loading required package: grid Loading required package: Matrix Loading required package: survival Attaching package: ‘survey’ The following object is masked from ‘package:graphics’: dotchart --- finished re-building ‘domain.Rnw’ --- re-building ‘epi.Rnw’ using Sweave Loading required package: grid Loading required package: Matrix Loading required package: survival Attaching package: ‘survey’ The following object is masked from ‘package:graphics’: dotchart Warning in eval(family$initialize) : non-integer #successes in a binomial glm! Warning in eval(family$initialize) : non-integer #successes in a binomial glm! Warning in eval(family$initialize) : non-integer #successes in a binomial glm! Error: processing vignette 'epi.Rnw' failed with diagnostics: chunk 7 Error in a$specials[[i]] : subscript out of bounds --- failed re-building ‘epi.Rnw’ --- re-building ‘pps.Rnw’ using Sweave Loading required package: grid Loading required package: Matrix Loading required package: survival Attaching package: ‘survey’ The following object is masked from ‘package:graphics’: dotchart --- finished re-building ‘pps.Rnw’ --- re-building ‘precalibrated.Rnw’ using Sweave Loading required package: grid Loading required package: Matrix Loading required package: survival Attaching package: ‘survey’ The following object is masked from ‘package:graphics’: dotchart --- finished re-building ‘precalibrated.Rnw’ --- re-building ‘qrule.Rnw’ using Sweave --- finished re-building ‘qrule.Rnw’ --- re-building ‘survey.Rnw’ using Sweave Loading required package: grid Loading required package: Matrix Loading required package: survival Attaching package: ‘survey’ The following object is masked from ‘package:graphics’: dotchart --- finished re-building ‘survey.Rnw’ SUMMARY: processing the following file failed: ‘epi.Rnw’ Error: Vignette re-building failed. Execution halted Flavor: r-devel-linux-x86_64-debian-gcc