version 3.5-8

Author: Terry M Therneau

DESCRIPTION

@@ -1,8 +1,8 @@
 Title: Survival Analysis
 Priority: recommended
 Package: survival
-Version: 3.5-7
-Date: 2023-08-12
+Version: 3.5-8
+Date: 2024-02-13
 Depends: R (>= 3.5.0)
 Imports: graphics, Matrix, methods, splines, stats, utils
 LazyData: Yes
@@ -22,12 +22,12 @@ Description: Contains the core survival analysis routines, including
 License: LGPL (>= 2)
 URL: https://github.com/therneau/survival
 NeedsCompilation: yes
-Packaged: 2023-08-13 13:14:48 UTC; therneau
+Packaged: 2024-02-13 23:24:58 UTC; therneau
 Author: Terry M Therneau [aut, cre],
   Thomas Lumley [ctb, trl] (original S->R port and R maintainer until
     2009),
   Atkinson Elizabeth [ctb],
   Crowson Cynthia [ctb]
 Maintainer: Terry M Therneau <therneau.terry@mayo.edu>
 Repository: CRAN
-Date/Publication: 2023-08-14 07:10:03 UTC
+Date/Publication: 2024-02-14 10:20:23 UTC

MD5

@@ -1,5 +1,5 @@
-89e7280b34651d91616ab89468230e8e *DESCRIPTION
-95773bb63fc2903652383dad14c5130b *NAMESPACE
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@@ -20,7 +20,7 @@ d9e503ad91694a2093718fb5393e522c *R/blogit.R
 8d2a46b60eca24003fc691a6e6a893d1 *R/brier.R
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@@ -66,7 +66,7 @@ f1eba83d6d0801904bfbbc577c17b7df *R/neardate.R
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@@ -94,7 +94,7 @@ a306fc683e7caf8f11b9c52d72ab430a *R/print.survfit.R
 cfc840167b14801ed0f5ca704a577192 *R/pseudo.R
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 f13ece60eca7461865a3efd1b9daffa7 *R/ratetableDate.R
 e7ff25f0ad7bad53552bc9d15e3b4fb8 *R/ratetableold.R
@@ -124,7 +124,7 @@ e202a5e249e9540dd0eada6199a39a00 *R/survConcordance.R
 e56e9ce40c37edc0fec6e0c77e73fc3f *R/survSplit.R
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 20ca6b16ed432517f2a5409803f4e32a *R/survexp.R
@@ -151,10 +151,10 @@ aef25cbfe8a6f43578d887f54ec115e8 *R/survfitms.R
 016e8b5dd0f4dfe6fb13b4f262bec247 *R/tcut.R
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 cda0ea84f065b219678a32e2947d1aa1 *R/yates.R
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 7ab17e8ecd5cec219e98686f8e04edfe *data/diabetic.rda
 862a5239dd76c7f0124e7eac703bd848 *data/flchain.rda
@@ -173,51 +173,51 @@ f6b7695a65d2503ac69826797c12061e *data/solder.rda
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 a87cc6e07b18736ffc490cfea48722f9 *man/Surv2.Rd
 fcc09d2b487b218b821423454b43970a *man/Surv2data.Rd
@@ -258,7 +258,7 @@ a17a8a4469cae8f32a0c980c478ba5ae *man/flchain.Rd
 e12cdf4b40fd81bf6c7690ec7a2a65dd *man/frailty.Rd
 03ecaac4eacbbbbc5b92d3b3513cd69a *man/gbsg.Rd
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 f7ad3e1700d98048b288ed73d7cf11b9 *man/is.ratetable.Rd
 2c480cbca6b287e697e2008905dc2714 *man/kidney.Rd
 007125656dba686dead87e88c6585a88 *man/levels.Surv.Rd
@@ -270,17 +270,17 @@ d9e7f7e73816b7de5ccfbfe0efd42895 *man/lung.Rd
 7ea33e0ef0740da761c655b0dc461aac *man/mgus2.Rd
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@@ -305,42 +305,42 @@ be32750af668c1bea9362b0bbe0614ae *man/quantile.survfit.Rd
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 14f8434ba1aeece36b0fdd1e7bbb5eca *man/transplant.Rd
 033ee961990ee412cf9ba50630110434 *man/udca.Rd
@@ -362,7 +362,7 @@ d1ee23fc09b6bffa9147fdbf1df191f4 *noweb/code.toc
 db8312f8406048ed9401af1674db9ced *noweb/coxph.Rnw
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@@ -478,7 +478,7 @@ b55447c3dbace7a78025931c85fbbce0 *src/survreg7.c
 1462b0ff0c70e67220bdfdf6f4b2cc11 *src/tmerge.c
 74f6ac54c5dc76cda6575cd88724e98f *src/zph1.c
 52be2135a54fb5a1bc2510dfc51e7615 *src/zph2.c
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@@ -602,8 +602,8 @@ a0ed2d78c2a25f00987ea551b7db0779 *tests/pseudo.R
 abc1d06f14f08ba65e04874ce1a471ae *tests/pseudo.Rout.save
 2f5dac3f5deaf51340f9743b804ce094 *tests/pspline.R
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 b11de7240223c5f41c2ed16d77279373 *tests/quantile.Rout.save
 3f721f6e1617f9ccabfd8242839866f2 *tests/r_lung.R
@@ -697,9 +697,9 @@ c82ecc64aea99282bc71ee98fe1d6b39 *vignettes/discrim.Rnw
 2cbd709bd670b43622db511e5072a1b4 *vignettes/other.Rnw
 03294e4a640c8f841f571a54b2503635 *vignettes/population.Rnw
 0a30d0a796fcd709d19cb9aaf1ae5adc *vignettes/redistribute.Rnw
-d1d0103d3630af04496496ed3051a28c *vignettes/refer.bib
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NAMESPACE

@@ -31,7 +31,7 @@ export(Surv, Surv2, Surv2data, aeqSurv, aareg, agreg.fit,
        ridge, royston, rsurvreg, rttright,statefig, strata, 
        survSplit, survcheck, survcondense, survdiff, survexp,  survfit,
        survfit0, survfit.formula,
-       coxsurv.fit, survfitKM, survfitCI,
+       coxsurv.fit, survfitKM,
        survobrien,  
        survpenal.fit, 
        survreg, survreg.control, survreg.fit,
@@ -84,10 +84,12 @@ S3method(c, Surv)
 S3method(c, Surv2)
 S3method(coef, concordance)
 S3method(coef, coxphms)
+S3method(coef, survfit)
 S3method(concordance, formula)
 S3method(concordance, lm)
 S3method(concordance, coxph)
 S3method(concordance, survreg)
+S3method(confint, survfit)
 S3method(density, Surv)
 S3method(dim, survfit)
 S3method(duplicated, Surv)
@@ -226,6 +228,7 @@ S3method(unique, Surv)
 S3method(vcov, cch)
 S3method(vcov, concordance)
 S3method(vcov, coxph)
+S3method(vcov, survfit)
 S3method(vcov, survreg)
 S3method(weights, coxph)
 S3method(weights, survreg)

R/clogit.R

@@ -38,8 +38,8 @@ clogit <- function(formula, data, weights, subset, na.action,
     # If the method is "exact", then case weights nor robust variance are
     #  possible
     if (method =="exact") {
-        if (missing(data)) temp <- terms(formula, special='cluster')
-        else temp <- terms(formula, special="cluster", data=data)
+        if (missing(data)) temp <- terms(formula, specials='cluster')
+        else temp <- terms(formula, specials="cluster", data=data)
         if (!is.null(attr(temp, 'specials')$cluster) && method=="exact")
             stop("robust variance plus the exact method is not supported")
 

R/plot.cox.zph.R

@@ -1,6 +1,6 @@
 plot.cox.zph <- function(x, resid=TRUE, se=TRUE, df=4, nsmo=40, 
                          var, xlab="Time", ylab="", lty=1:2, col=1, lwd=1,
-                         hr = FALSE, ...) {
+                         hr = FALSE, plot=TRUE, ...) {
     xx <- x$x
     yy <- x$y
     df <- max(df)     # in case df is a vector
@@ -22,6 +22,7 @@ plot.cox.zph <- function(x, resid=TRUE, se=TRUE, df=4, nsmo=40,
 	if  (any(is.na(var)) || max(var)>nvar || min(var) <1)
 	    stop("Invalid variable requested")
     }
+    if (!plot) resid <- FALSE   # only return the curve
 
     #
     # Figure out a 'good' set of x-axis labels.  Find 8 equally spaced
@@ -83,6 +84,9 @@ plot.cox.zph <- function(x, resid=TRUE, se=TRUE, df=4, nsmo=40,
         doxaxis <- TRUE
         if (!is.null(plotpar$xaxt)) doxaxis <- FALSE
 
+        if (!plot)  # return the curve
+            return(list(x=pred.x, y=cbind(yhat, yup, ylow)))
+4
         if (!hr) {
             if (x$transform=='identity')
                 plot(range(xx), yr, type='n', xlab=xlab, ylab=ylab[i], ...)

R/quantile.survfit.R

@@ -54,6 +54,9 @@ quantile.survfit <- function(x, probs=c(.25, .5, .75), conf.int=TRUE,
                              scale, 
                              tolerance= sqrt(.Machine$double.eps), ...) {
     if (!inherits(x, "survfit")) stop("Must be a survfit object")
+    if (inherits(x, "survfitms")) 
+        stop("quantiles are not a well defined quantity for multi-state models")
+
     if (any(!is.numeric(probs)) || any(is.na(probs)))
         stop("invalid probability")
     if (any(probs <0 | probs >1)) stop("Invalid probability")

R/survcondense.R

@@ -16,7 +16,7 @@ survcondense <- function(formula, data, subset, weights, na.action= na.pass, id,
     Terms <- if (missing(data)) terms(formula, specials=ss) else
                  terms(formula, specials=ss, data=data)
     if (length(attr(Terms, "specials")$cluster) >0)
-        stop("function does not handle cluster terms")
+        stop("function does not handle cluster() terms")
 
     indx <- match(c("formula", "data", "weights", "subset","id"), 
                   names(Call), nomatch=0)
@@ -47,10 +47,6 @@ survcondense <- function(formula, data, subset, weights, na.action= na.pass, id,
     Ydup <- c(Y[index[-1], 1]== Y[index[-n], 2], FALSE)
 
     droprow <- unname(Xdup & Ydup)
-    if (!any(droprow)) {  # toss nothing
-        if (!missing(subset)) return(subset(data, subset))
-        else return(data)
-    }
 
     # There will often be clusters of rows with droprow=TRUE, the start time
     #  for the first row of said cluster is moved to the first row after
@@ -60,7 +56,8 @@ survcondense <- function(formula, data, subset, weights, na.action= na.pass, id,
 
     # The last rle value is always a FALSE
     # Two special cases first
-    if (length(temp2)==2) { # only deletion is the very first 1 or more rows
+    if (!any(droprow)){} 
+    else if (length(temp2)==2) { # only deletion is the very first k rows
         Y[temp2[1] +1, 1] = Y[1, 1]
     } else if (length(temp2) ==3) { # a single block somewhere in the middle
         Y[temp2[2] +1, 1] = Y[temp2[1] +1, 1]

R/xtras.R

@@ -96,3 +96,13 @@ survflag <- function(y, id) {
     flag
 }
 
+
+# Dummy methods, to create an informative error message
+coef.survfit <- function(object, ...) 
+    stop("coef method not applicable for survfit objects")
+vcov.survfit <- function(object, ...) 
+    stop("vcov method not applicable for survfit objects")
+confint.survfit <- function(object, ...)
+    stop(paste("confint method not defined for survfit objects," ,
+         "use quantile for confidence intervals of the median survival"))
+