diff -Nru survival-2.37-6/DESCRIPTION survival-2.37-7/DESCRIPTION --- survival-2.37-6/DESCRIPTION 2014-01-16 15:31:10.000000000 +0000 +++ survival-2.37-7/DESCRIPTION 2014-01-22 16:49:47.000000000 +0000 @@ -2,16 +2,15 @@ Maintainer: Terry M Therneau Priority: recommended Package: survival -Version: 2.37-6 +Version: 2.37-7 Depends: stats, utils, graphics, splines, R (>= 2.13.0) -Suggests: survey LazyData: Yes LazyLoad: Yes ByteCompile: Yes -Authors@R: c(person(c("Terry", "M"), "Therneau", +Authors@R: c(person(c("Terry", "M"), "Therneau", email="therneau.terry@mayo.edu", role=c("aut", "cre")), - person("Lumley", "Thomas", role=c("ctb", "trl"), + person("Thomas", "Lumley", role=c("ctb", "trl"), comment="original S->R port and maintainer until 2009")) Description: survival analysis: descriptive statistics, two-sample tests, parametric accelerated failure models, Cox model. Delayed entry @@ -19,9 +18,9 @@ models. Case-cohort designs. License: LGPL (>= 2) URL: http://r-forge.r-project.org -Packaged: 2014-01-15 19:46:10 UTC; therneau +Packaged: 2014-01-22 13:49:28 UTC; therneau Author: Terry M Therneau [aut, cre], - Lumley Thomas [ctb, trl] (original S->R port and maintainer until 2009) + Thomas Lumley [ctb, trl] (original S->R port and maintainer until 2009) NeedsCompilation: yes Repository: CRAN -Date/Publication: 2014-01-16 16:31:10 +Date/Publication: 2014-01-22 17:49:47 diff -Nru survival-2.37-6/MD5 survival-2.37-7/MD5 --- survival-2.37-6/MD5 2014-01-16 15:31:11.000000000 +0000 +++ survival-2.37-7/MD5 2014-01-22 16:49:49.000000000 +0000 @@ -1,4 +1,4 @@ -3403a51653d40c41ba8cae9b56879806 *DESCRIPTION +c8580cbd1325b9c425facded21a52256 *DESCRIPTION b8d55830bfb9432bad611b56767092ec *NAMESPACE 560a44987824f6e66d262cd7769043b3 *R/Surv.S 848a740b51619bdc8e5034a7ea9a7b06 *R/aareg.S @@ -52,7 +52,7 @@ 3f2cf73eb9c5f8bbf6c63a9b4a74d090 *R/model.matrix.coxph.R 5220681f176b87fb822910dea854ccf4 *R/plot.aareg.S bbc7b13d91874c741e88b7cdb761aa5a *R/plot.cox.zph.S -a07942df5cb61d125c737565f00310db *R/plot.survfit.R +154e569c638afb6d0acc86b9b53b07cb *R/plot.survfit.R e9a3b797eced2c1e269467c1122b5d24 *R/predict.coxph.R 81cb6184133a24d2847372f9b7d3ed2e *R/predict.coxph.penal.S 88a947c3450372ff0b88fd297554ce64 *R/predict.survreg.S @@ -145,17 +145,17 @@ d4b78dd46512d982683f6bb2a025aa9a *data/veteran.rda 01efa4cd2eb579996180213b1a004d02 *inst/CITATION 3e8ebae349953a3b7a665eecce562802 *inst/COPYRIGHTS -a1479bc161ffbdfd16dc2002341a09fc *inst/NEWS.Rd -ea9869ec8a01cb589a6ab80955d0752f *inst/doc/adjcurve.R -b7956a44a4ccd9098932b8d760a49820 *inst/doc/adjcurve.Rnw -dd51f3b8829a56df65d03116fd76b08e *inst/doc/adjcurve.pdf -ce90d9335ebfef31ec3c4a7827ca3ee9 *inst/doc/sourcecode.pdf +39e28c75bc4f5dd87db12cff861575b9 *inst/NEWS.Rd +d3fb174c4c7344fd1e633ae18564cbe0 *inst/doc/adjcurve.R +f7927f2f78ed007021a9b34047a10509 *inst/doc/adjcurve.Rnw +5d32773d4ba2942937567fe03ba0c2fe *inst/doc/adjcurve.pdf +96fdb34c9c8cd174fa2c146feb5f6e05 *inst/doc/sourcecode.pdf 7e7ee9ce10ba460e3c5eb33014d24bc7 *inst/doc/tests.R 5fb51c8731bedc07042dfd2c2625a066 *inst/doc/tests.Rnw -f487295593173ada3b8b7bf8c27b0179 *inst/doc/tests.pdf +8a6a9b5b4f36a729897521c839c2beaf *inst/doc/tests.pdf 321a774c0e73e4316c92f8fe59b32bb6 *inst/doc/timedep.R f0d037543ded6fd0f5456dac8cf5b661 *inst/doc/timedep.Rnw -0bfb0ada0cb6874fd6c0d2bd1a10c252 *inst/doc/timedep.pdf +72ef1e771772bef77450fcba90504048 *inst/doc/timedep.pdf ac297959a2f3093d13819580a6292410 *inst/doc/validate.pdf e3e0c8f7470da537df515c7e9bf89280 *man/Surv.Rd e1b4f2135554802fd7d56872fcbb0d42 *man/aareg.Rd @@ -450,7 +450,7 @@ 8237935a710efe7ee122ca5b05ef56b1 *tests/tt.Rout.save b1dd6e9b7bf7a5a26e8879c3f7fb03d9 *tests/turnbull.R d0e0c0f2ef0cbc69aebb7800b5fee3a2 *tests/turnbull.Rout.save -b7956a44a4ccd9098932b8d760a49820 *vignettes/adjcurve.Rnw +f7927f2f78ed007021a9b34047a10509 *vignettes/adjcurve.Rnw 06d6eaadbc38228c840e1c0e968643bc *vignettes/raheart.rda c3162ad5bf37d039ec9c0b4298b8c6ee *vignettes/refer.bib 5fb51c8731bedc07042dfd2c2625a066 *vignettes/tests.Rnw diff -Nru survival-2.37-6/R/plot.survfit.R survival-2.37-7/R/plot.survfit.R --- survival-2.37-6/R/plot.survfit.R 2014-01-15 19:45:27.000000000 +0000 +++ survival-2.37-7/R/plot.survfit.R 2014-01-22 13:48:46.000000000 +0000 @@ -124,7 +124,8 @@ 'cumhaz'=function(x) -log(x), 'cloglog'=function(x) log(-log(x)), 'pct' = function(x) x*100, - 'logpct'= function(x) 100*x, + 'logpct'= function(x) 100*x, #special case further below + 'identity'= function(x) x, stop("Unrecognized function argument") ) } @@ -214,7 +215,7 @@ } tempy <- c(tempy, firsty) } - else tempy <- c(range(ssurv[is.finite(ssurv)] ), firsty) + else tempy <- range(ssurv, firsty, finite=TRUE, na.rm=TRUE) if (missing(fun)) { tempx <- c(tempx, firstx) @@ -224,8 +225,9 @@ # # Draw the basic box # - plot(range(tempx), range(tempy)*yscale, type='n', log=logax, - xlab=xlab, ylab=ylab, xaxs=xaxs,...) + plot(range(tempx, finite=TRUE, na.rm=TRUE), + range(tempy, finite=TRUE, na.rm=TRUE)*yscale, + type='n', log=logax, xlab=xlab, ylab=ylab, xaxs=xaxs,...) if(yscale != 1) { if (ylog) par(usr =par("usr") -c(0, 0, log10(yscale), log10(yscale))) @@ -411,7 +413,8 @@ 'cumhaz'=function(x) -log(x), 'cloglog'=function(x) log(-log(x)), 'pct' = function(x) x*100, - 'logpct'= function(x) 100*x, + 'logpct'= function(x) 100*x, #special case further below + 'identity'= function(x) x, stop("Unrecognized function argument") ) } @@ -648,7 +651,8 @@ 'cumhaz'=function(x) -log(x), 'cloglog'=function(x) log(-log(x)), 'pct' = function(x) x*100, - 'logpct'= function(x) 100*x, + 'logpct'= function(x) 100*x, #special case further below + 'identity'= function(x) x, stop("Unrecognized function argument") ) } diff -Nru survival-2.37-6/debian/changelog survival-2.37-7/debian/changelog --- survival-2.37-6/debian/changelog 2014-01-24 01:26:15.000000000 +0000 +++ survival-2.37-7/debian/changelog 2014-01-24 01:26:16.000000000 +0000 @@ -1,8 +1,14 @@ -survival (2.37-6-1~lucid1~ppa1) lucid; urgency=low +survival (2.37-7-1lucid0) lucid; urgency=low - * No-change backport to lucid + * Compilation for Ubuntu 10.04.4 LTS - -- Michael Rutter Mon, 20 Jan 2014 18:49:29 -0500 + -- Michael Rutter Fri, 24 Jan 2014 00:20:21 +0000 + +survival (2.37-7-1) unstable; urgency=low + + * New upstream release + + -- Dirk Eddelbuettel Wed, 22 Jan 2014 14:24:35 -0600 survival (2.37-6-1) unstable; urgency=low diff -Nru survival-2.37-6/inst/NEWS.Rd survival-2.37-7/inst/NEWS.Rd --- survival-2.37-6/inst/NEWS.Rd 2014-01-15 19:45:23.000000000 +0000 +++ survival-2.37-7/inst/NEWS.Rd 2014-01-22 13:48:42.000000000 +0000 @@ -1,5 +1,17 @@ \name{NEWS} \title{NEWS file for the survival package} +\section{Changes in version 2.37-7}{ + \itemize{ + \item Remove a dependency on the survey package from the adjusted + survival curves vignette, at the request of CRAN. (The base + + required bundle needs to be capable of a stand-alone build.) + + \item Fix error in calcuation of the y-axis range for survival curve + plots whenever the "fun" argument could produce infinite values, + e.g., complimentary log-log plots transform 1 to -Inf. Pointed out + by Eva Boj del Val. (Add finite=TRUE to range() call). +}} + \section{Changes in version 2.37-6}{ \itemize{ \item The plot for competing risk curves could have a spurious diff -Nru survival-2.37-6/inst/doc/adjcurve.R survival-2.37-7/inst/doc/adjcurve.R --- survival-2.37-6/inst/doc/adjcurve.R 2014-01-15 19:46:10.000000000 +0000 +++ survival-2.37-7/inst/doc/adjcurve.R 2014-01-22 13:49:28.000000000 +0000 @@ -192,21 +192,17 @@ ################################################### -### code chunk number 14: adjcurve.Rnw:495-508 +### code chunk number 14: adjcurve.Rnw:498-507 ################################################### id <- 1:nrow(fdata) cfit <- coxph(Surv(futime, death) ~ group + cluster(id), data=fdata, weight=rwt) summary(cfit)$robscore -require(survey) -sdes <- svydesign(id = ~0, weights=~rwt, data=fdata) -dfit <- svykm(Surv(futime, death) ~ group, design=sdes) -# the next line is painfully slow for this large a data set -#dfit <- svykm(Surv(futime, death) ~ group, design=sdes, se=TRUE) -# coming in a future survival release -#sfit3 <- survfit(Surv(futime, death) ~ group + cluster(id), -# data=fdata, weight=rwt) +if (exists("svykm")) { #true if the survey package is loaded + sdes <- svydesign(id = ~0, weights=~rwt, data=fdata) + dfit <- svykm(Surv(futime, death) ~ group, design=sdes, se=TRUE) +} ################################################### @@ -265,7 +261,7 @@ ################################################### -### code chunk number 17: adjcurve.Rnw:639-649 +### code chunk number 17: adjcurve.Rnw:638-648 ################################################### # compute new weights wtscale <- table(fdata$group)/ tapply(fdata$rwt, fdata$group, sum) @@ -312,7 +308,7 @@ ################################################### -### code chunk number 20: adjcurve.Rnw:774-775 +### code chunk number 20: adjcurve.Rnw:773-774 ################################################### survdiff(Surv(futime, death) ~ group + strata(age2, sex), fdata) @@ -353,7 +349,7 @@ ################################################### -### code chunk number 23: adjcurve.Rnw:886-893 +### code chunk number 23: adjcurve.Rnw:885-892 ################################################### tfit <- survfit(cfit4a, newdata=tdata, se.fit=FALSE) curves <- vector('list', 3) @@ -392,7 +388,7 @@ ################################################### -### code chunk number 25: adjcurve.Rnw:964-972 +### code chunk number 25: adjcurve.Rnw:963-971 ################################################### getOption("SweaveHooks")[["fig"]]() obs <- with(fdata, tapply(death, list(age2, sex, group), sum)) @@ -406,7 +402,7 @@ ################################################### -### code chunk number 26: adjcurve.Rnw:988-1000 +### code chunk number 26: adjcurve.Rnw:987-999 ################################################### cfit5a <- coxph(Surv(futime, death) ~ group:age +sex + strata(group), fdata) diff -Nru survival-2.37-6/inst/doc/adjcurve.Rnw survival-2.37-7/inst/doc/adjcurve.Rnw --- survival-2.37-6/inst/doc/adjcurve.Rnw 2014-01-15 19:46:10.000000000 +0000 +++ survival-2.37-7/inst/doc/adjcurve.Rnw 2014-01-22 13:49:28.000000000 +0000 @@ -486,29 +486,28 @@ Correct standard errors for the curves are readily computed using methods from that literature, and are available in some software packages. In R the \texttt{svykm} routine in the \texttt{survey} package handles both this -simple case and more complex sampling schemes. +simple case and more complex sampling schemes. Tests of the curves can be done using a weighted Cox model; the robust variance produced by \texttt{coxph} is identical to the standard Horvitz-Thompsen variance estimate used in survey sampling \cite{Binder92}. The score test from \texttt{coxph} is equivalent to the log-rank test that is often used to label curves. +(In the example below the sykm function is only run if the survey package +is already loaded, as the variance calculation is very slow for this large +data set.) <<>>= id <- 1:nrow(fdata) cfit <- coxph(Surv(futime, death) ~ group + cluster(id), data=fdata, weight=rwt) summary(cfit)$robscore -require(survey) -sdes <- svydesign(id = ~0, weights=~rwt, data=fdata) -dfit <- svykm(Surv(futime, death) ~ group, design=sdes) -# the next line is painfully slow for this large a data set -#dfit <- svykm(Surv(futime, death) ~ group, design=sdes, se=TRUE) -# coming in a future survival release -#sfit3 <- survfit(Surv(futime, death) ~ group + cluster(id), -# data=fdata, weight=rwt) +if (exists("svykm")) { #true if the survey package is loaded + sdes <- svydesign(id = ~0, weights=~rwt, data=fdata) + dfit <- svykm(Surv(futime, death) ~ group, design=sdes, se=TRUE) +} @ Note: including the \texttt{cluster} term in the coxph call causes it to -treat the weights as resampling values and thus to use the proper +treat the weights as resampling values and thus use the proper survey sampling style variance. The default without that term would be to treat the case weights as replication counts. Binary files /tmp/aAlKveYe1J/survival-2.37-6/inst/doc/adjcurve.pdf and /tmp/geWtgFloME/survival-2.37-7/inst/doc/adjcurve.pdf differ Binary files /tmp/aAlKveYe1J/survival-2.37-6/inst/doc/sourcecode.pdf and /tmp/geWtgFloME/survival-2.37-7/inst/doc/sourcecode.pdf differ Binary files /tmp/aAlKveYe1J/survival-2.37-6/inst/doc/tests.pdf and /tmp/geWtgFloME/survival-2.37-7/inst/doc/tests.pdf differ Binary files /tmp/aAlKveYe1J/survival-2.37-6/inst/doc/timedep.pdf and /tmp/geWtgFloME/survival-2.37-7/inst/doc/timedep.pdf differ diff -Nru survival-2.37-6/vignettes/adjcurve.Rnw survival-2.37-7/vignettes/adjcurve.Rnw --- survival-2.37-6/vignettes/adjcurve.Rnw 2014-01-15 19:45:23.000000000 +0000 +++ survival-2.37-7/vignettes/adjcurve.Rnw 2014-01-22 13:48:42.000000000 +0000 @@ -486,29 +486,28 @@ Correct standard errors for the curves are readily computed using methods from that literature, and are available in some software packages. In R the \texttt{svykm} routine in the \texttt{survey} package handles both this -simple case and more complex sampling schemes. +simple case and more complex sampling schemes. Tests of the curves can be done using a weighted Cox model; the robust variance produced by \texttt{coxph} is identical to the standard Horvitz-Thompsen variance estimate used in survey sampling \cite{Binder92}. The score test from \texttt{coxph} is equivalent to the log-rank test that is often used to label curves. +(In the example below the sykm function is only run if the survey package +is already loaded, as the variance calculation is very slow for this large +data set.) <<>>= id <- 1:nrow(fdata) cfit <- coxph(Surv(futime, death) ~ group + cluster(id), data=fdata, weight=rwt) summary(cfit)$robscore -require(survey) -sdes <- svydesign(id = ~0, weights=~rwt, data=fdata) -dfit <- svykm(Surv(futime, death) ~ group, design=sdes) -# the next line is painfully slow for this large a data set -#dfit <- svykm(Surv(futime, death) ~ group, design=sdes, se=TRUE) -# coming in a future survival release -#sfit3 <- survfit(Surv(futime, death) ~ group + cluster(id), -# data=fdata, weight=rwt) +if (exists("svykm")) { #true if the survey package is loaded + sdes <- svydesign(id = ~0, weights=~rwt, data=fdata) + dfit <- svykm(Surv(futime, death) ~ group, design=sdes, se=TRUE) +} @ Note: including the \texttt{cluster} term in the coxph call causes it to -treat the weights as resampling values and thus to use the proper +treat the weights as resampling values and thus use the proper survey sampling style variance. The default without that term would be to treat the case weights as replication counts.