Binary files 7.3-57-1/build/partial.rdb and 7.3-58.1-1/build/partial.rdb differ diff -pruN 7.3-57-1/ChangeLog 7.3-58.1-1/ChangeLog --- 7.3-57-1/ChangeLog 1970-01-01 00:00:00.000000000 +0000 +++ 7.3-58.1-1/ChangeLog 2022-07-27 05:25:16.000000000 +0000 @@ -0,0 +1,90 @@ +7.3-58.1 (released 2022-07-27) + DESCRIPTION: No longer suggest gamaair. + tests/polr.R: use named .pdf file. + tests/glmmPQL.R, solr.rda: ship data file, skip if no nlme. + +7.3-58 (released 2022-07-14) + glmmPQL: work around disabling of offsets in nlme::lme, + following a request from Simon Wood. + glmmPQL: Add any offset to fitted values. + tests/glmmPQL.R: add (modified) example from Simon Wood. + DESCRIPTION: add Suggests: gamair for that example. + tests/confit.R: name PDF file + tests/scripts.R: mention packages needed not in Suggests. + inst/scripts/ch{11,13}.R tweaks. + inst/scripts/ch15.R: switch from akima to interp. + man/*.Rd: change references to third edition to fourth. + +7.3-57.2 (released 2022-07-10, R-devel only) + src/MASS.c: #include rather than rely on R.h. + man/glmmPQL.Rd: example no longer attaches nlme. + +7.3-57.1 (released 2022-05-30, R-devel only) + Start ChangeLog. + src/lqs.c: clang defines __GNUC__, so rule out. + src/MASS.c: replace Sfloat/Sint. + +7.3-57 (released 2022-04-23, after R 4.2.0) + add formula method for glmmPQL (suggested by Sebastian Meyer) + update reference output for LAPACK 3.10.x, more use of IGNORE_RDIFF. + add pragmas to src/lqs.c to avoid mis-optimization in pre-gcc12 + (and before at high optimization levels). + add check for gcc12 woes to tests/cov.mcd.R + remove basckslash from \$ in Boston.Rd and Cars93.Rd + +7.3-56 (released 2022-03-23) + offsets on lme have been disabled + +7.3-55 (released 2022-01-13) + src/lqs.c include float.h explicitly (for STRICT_R_HEADERS) + src/MASS.c: prefer R_Calloc etc. + Update de, fr translations. + +7.3-54 (released 2021-05-03) + Update .pot files, fr translations. + +7.3-53.1 (released 2021-02-12) + Use \doi rather than \url, so bump minimum R requirement. + Update .pot files. + +7.3-53 (released 2020-09-09) + allaw for possible integer overflow + mention hard limit in cov.rob.Rd + expaand description of 'data' args. + +7.3-52 (released 2020-08-18) + rlm with offset term + correct description in newcomb.Rd + typo in cats.Rd + +7.3-51.[1-6] (released 2018-11-01 to 2020-04-26) + typo in man/cats.Rd + Use RDIFF markup + add it translations + change .Rout.save for change in RNG in R 3.6.0 + change .Rout.save for survival changes + +7.3-51 (released 2018-10-16) + replace broken URL + remove S-style example + +7.3-50 (released 2018-04-30) + survival changed output + update .pot files + +7.3-49 (released 2018-02-23) + remove 'f' from fitdistr + make tests/lme4.R conditional on nlme + +7.3-48 (released 2017-12-25) + \testonly -> \dontshow + move extractAIC methods to nlme. + +7.3-47 (released 2017-04-21) + Cosmetics + Check for integer overflow in density binning. + +7.3-46 (released 2017-02-14) + Avoid partial match in rlm.default. + Include headers explicitly in MASS.c and lqs.c + Use R_forceSymbols(dll, TRUE) uncondiitonally. diff -pruN 7.3-57-1/debian/changelog 7.3-58.1-1/debian/changelog --- 7.3-57-1/debian/changelog 2022-04-22 18:37:54.000000000 +0000 +++ 7.3-58.1-1/debian/changelog 2022-08-04 17:51:04.000000000 +0000 @@ -1,3 +1,18 @@ +r-cran-mass (7.3-58.1-1) unstable; urgency=medium + + * New upstream release + + -- Dirk Eddelbuettel Thu, 04 Aug 2022 12:51:04 -0500 + +r-cran-mass (7.3-58-1) unstable; urgency=medium + + * New upstream release + + * debian/control: Set Build-Depends: to current R version + * debian/control: Set Standards-Version: to current version + + -- Dirk Eddelbuettel Thu, 14 Jul 2022 06:43:39 -0500 + r-cran-mass (7.3-57-1) unstable; urgency=medium * New upstream release diff -pruN 7.3-57-1/debian/control 7.3-58.1-1/debian/control --- 7.3-57-1/debian/control 2022-04-22 18:37:37.000000000 +0000 +++ 7.3-58.1-1/debian/control 2022-07-14 11:43:54.000000000 +0000 @@ -2,8 +2,8 @@ Source: r-cran-mass Section: gnu-r Priority: optional Maintainer: Dirk Eddelbuettel -Build-Depends: debhelper-compat (= 11), r-base-dev (>= 4.2.0), dh-r -Standards-Version: 4.6.0 +Build-Depends: debhelper-compat (= 11), r-base-dev (>= 4.2.1), dh-r +Standards-Version: 4.6.1 Vcs-Browser: https://salsa.debian.org/edd/r-cran-mass Vcs-Git: https://salsa.debian.org/edd/r-cran-mass.git Homepage: https://cran.r-project.org/package=MASS diff -pruN 7.3-57-1/DESCRIPTION 7.3-58.1-1/DESCRIPTION --- 7.3-57-1/DESCRIPTION 2022-04-22 11:45:27.000000000 +0000 +++ 7.3-58.1-1/DESCRIPTION 2022-08-03 15:06:59.000000000 +0000 @@ -1,8 +1,8 @@ Package: MASS Priority: recommended -Version: 7.3-57 -Date: 2022-04-05 -Revision: $Rev: 3564 $ +Version: 7.3-58.1 +Date: 2022-07-27 +Revision: $Rev: 3606 $ Depends: R (>= 3.3.0), grDevices, graphics, stats, utils Imports: methods Suggests: lattice, nlme, nnet, survival @@ -24,7 +24,7 @@ License: GPL-2 | GPL-3 URL: http://www.stats.ox.ac.uk/pub/MASS4/ Contact: NeedsCompilation: yes -Packaged: 2022-04-19 04:13:16 UTC; ripley +Packaged: 2022-07-27 05:37:13 UTC; ripley Author: Brian Ripley [aut, cre, cph], Bill Venables [ctb], Douglas M. Bates [ctb], @@ -33,4 +33,4 @@ Author: Brian Ripley [aut, cre, cph], David Firth [ctb] Maintainer: Brian Ripley Repository: CRAN -Date/Publication: 2022-04-22 11:45:27 UTC +Date/Publication: 2022-08-03 15:06:59 UTC diff -pruN 7.3-57-1/inst/scripts/ch11.R 7.3-58.1-1/inst/scripts/ch11.R --- 7.3-57-1/inst/scripts/ch11.R 2013-07-18 09:32:11.000000000 +0000 +++ 7.3-58.1-1/inst/scripts/ch11.R 2022-07-09 16:41:15.000000000 +0000 @@ -31,7 +31,8 @@ loadings(lcrabs.pca) lcrabs.pc <- predict(lcrabs.pca) dimnames(lcrabs.pc) <- list(NULL, paste("PC", 1:5, sep = "")) -if(FALSE) { # needs interaction with XGobi, or, better, rggobi +if(FALSE) { ## needs interaction with XGobi, or, better, rggobi + ## Both have been withdrawn for R. library(xgobi) xgobi(lcrabs, colors = c("SkyBlue", "SlateBlue", "Orange", "Red")[rep(1:4, each = 50)]) diff -pruN 7.3-57-1/inst/scripts/ch13.R 7.3-58.1-1/inst/scripts/ch13.R --- 7.3-57-1/inst/scripts/ch13.R 2012-05-15 23:17:48.000000000 +0000 +++ 7.3-58.1-1/inst/scripts/ch13.R 2022-07-09 16:35:33.000000000 +0000 @@ -164,8 +164,9 @@ coxph(Surv(start, stop, event) ~ transpl stan1 <- coxph(Surv(start, stop, event) ~ strata(transplant) + year + year:transplant + age + surgery, heart) -par(mfrow=c(1,2), pty="s") -plot(survfit(stan1), conf.int = TRUE, log = TRUE, lty = c(1, 3), col = 2:3) +par(mfrow = c(1,2), pty = "s") +## failed 2022-07 +## plot(survfit(stan1), conf.int = TRUE, log = TRUE, lty = c(1, 3), col = 2:3) #legend(locator(1), c("before", "after"), lty = c(1, 3), col= 2:3) attach(heart) @@ -238,10 +239,11 @@ plot(aids2.surv[c(1, 5, 6, 8)], mark.tim #legend(locator(1), levels(T.categ)[c(1, 5, 6, 8)], lty = 1:4, col = 2:5) par(mfrow=c(1,1), pty="m") -cases <- diff(c(0,idno)) != 0 -aids.res <- residuals(aids.cox, collapse = idno) -scatter.smooth(age[cases], aids.res, xlab = "age", - ylab="martingale residual") +## fails 2022-07 +#cases <- diff(c(0,idno)) != 0 +#aids.res <- residuals(aids.cox, collapse = idno) +#scatter.smooth(age[cases], aids.res, xlab = "age", +# ylab = "martingale residual") age2 <- cut(age, c(-1, 15, 30, 40, 50, 60, 100)) c.age <- factor(as.numeric(age2), labels = c("0-15", "16-30", diff -pruN 7.3-57-1/inst/scripts/ch15.R 7.3-58.1-1/inst/scripts/ch15.R --- 7.3-57-1/inst/scripts/ch15.R 2012-05-15 23:17:48.000000000 +0000 +++ 7.3-58.1-1/inst/scripts/ch15.R 2022-06-04 10:33:50.000000000 +0000 @@ -76,15 +76,15 @@ contour(topo.mar$x,topo.mar$y,topo.lo$se title("Loess degree = 1") points(topo) -library(akima) +library(interp) # was akima, interp.old() par(mfrow = c(1, 2), pty= "s") -topo.int <- interp.old(topo$x, topo$y, topo$z) +topo.int <- interp(topo$x, topo$y, topo$z) eqscplot(topo.int, xlab = "interp default", ylab = "", type = "n") contour(topo.int, levels = seq(600, 1000, 25), add = TRUE) points(topo) topo.mar <- list(x = seq(0, 6.5, 0.1), y = seq(0, 6.5, 0.1)) -topo.int2 <- interp.old(topo$x, topo$y, topo$z, topo.mar$x, topo.mar$y, - ncp = 4, extrap = TRUE) +topo.int2 <- interp(topo$x, topo$y, topo$z, topo.mar$x, topo.mar$y, + extrap = TRUE) # was ncp = 4. eqscplot(topo.int2, xlab = "interp", ylab = "", type = "n") contour(topo.int2, levels = seq(600, 1000, 25), add = TRUE) points(topo) diff -pruN 7.3-57-1/man/accdeaths.Rd 7.3-58.1-1/man/accdeaths.Rd --- 7.3-57-1/man/accdeaths.Rd 2012-05-15 23:17:48.000000000 +0000 +++ 7.3-58.1-1/man/accdeaths.Rd 2022-07-11 11:13:51.000000000 +0000 @@ -23,8 +23,7 @@ accdeaths Springer, New York. } \references{ - Venables, W. N. and Ripley, B. D. (1999) - \emph{Modern Applied Statistics with S-PLUS.} Third - Edition. Springer. + Venables, W. N. and Ripley, B. D. (2002) + \emph{Modern Applied Statistics with S-PLUS.} Fourth Edition. Springer. } \keyword{datasets} diff -pruN 7.3-57-1/man/Animals.Rd 7.3-58.1-1/man/Animals.Rd --- 7.3-57-1/man/Animals.Rd 2012-05-15 23:17:48.000000000 +0000 +++ 7.3-58.1-1/man/Animals.Rd 2022-07-11 11:11:44.000000000 +0000 @@ -1,5 +1,5 @@ % file MASS/man/animals.Rd -% copyright (C) 1994-9 W. N. Venables and B. D. Ripley +% copyright (C) 1994-2022 W. N. Venables and B. D. Ripley % \name{Animals} \alias{Animals} @@ -23,7 +23,7 @@ Animals } } \note{ - The name \code{Animals} avoids conflicts with a system dataset + The name \code{Animals} avoided conflicts with a system dataset \code{animals} in S-PLUS 4.5 and later. } \source{ @@ -32,8 +32,7 @@ Animals Wiley, p. 57. } \references{ - Venables, W. N. and Ripley, B. D. (1999) - \emph{Modern Applied Statistics with S-PLUS.} Third - Edition. Springer. + Venables, W. N. and Ripley, B. D. (2002) + \emph{Modern Applied Statistics with S-PLUS.} Fourth Edition. Springer. } \keyword{datasets} diff -pruN 7.3-57-1/man/biopsy.Rd 7.3-58.1-1/man/biopsy.Rd --- 7.3-57-1/man/biopsy.Rd 2012-05-15 23:17:48.000000000 +0000 +++ 7.3-58.1-1/man/biopsy.Rd 2022-07-11 11:14:09.000000000 +0000 @@ -60,8 +60,7 @@ biopsy \bold{1}, pp. 23--34 (Gordon & Breach Science Publishers). } \references{ - Venables, W. N. and Ripley, B. D. (1999) - \emph{Modern Applied Statistics with S-PLUS.} Third - Edition. Springer. + Venables, W. N. and Ripley, B. D. (2002) + \emph{Modern Applied Statistics with S-PLUS.} Fourth Edition. Springer. } \keyword{datasets} diff -pruN 7.3-57-1/man/cabbages.Rd 7.3-58.1-1/man/cabbages.Rd --- 7.3-57-1/man/cabbages.Rd 2012-05-15 23:17:48.000000000 +0000 +++ 7.3-58.1-1/man/cabbages.Rd 2022-07-11 11:14:32.000000000 +0000 @@ -39,8 +39,7 @@ cabbages Dr Gertrude M Cox.) } \references{ - Venables, W. N. and Ripley, B. D. (1999) - \emph{Modern Applied Statistics with S-PLUS.} Third - Edition. Springer. + Venables, W. N. and Ripley, B. D. (2002) + \emph{Modern Applied Statistics with S-PLUS.} Fourth Edition. Springer. } \keyword{datasets} diff -pruN 7.3-57-1/man/Cars93.Rd 7.3-58.1-1/man/Cars93.Rd --- 7.3-57-1/man/Cars93.Rd 2022-04-19 04:12:29.000000000 +0000 +++ 7.3-58.1-1/man/Cars93.Rd 2022-07-11 11:12:09.000000000 +0000 @@ -119,8 +119,7 @@ Cars93 % \url{http://www.amstat.org/publications/jse/v1n1/datasets.lock.html}. } \references{ - Venables, W. N. and Ripley, B. D. (1999) - \emph{Modern Applied Statistics with S-PLUS.} Third - Edition. Springer. + Venables, W. N. and Ripley, B. D. (2002) + \emph{Modern Applied Statistics with S-PLUS.} Fourth Edition. Springer. } \keyword{datasets} diff -pruN 7.3-57-1/man/cov.trob.Rd 7.3-58.1-1/man/cov.trob.Rd --- 7.3-57-1/man/cov.trob.Rd 2012-05-15 23:17:48.000000000 +0000 +++ 7.3-58.1-1/man/cov.trob.Rd 2022-07-11 11:14:58.000000000 +0000 @@ -72,9 +72,8 @@ The number of iterations used. \emph{Communications in Statistics---Simulation and Computation} \bold{23}, 441--453. - Venables, W. N. and Ripley, B. D. (1999) - \emph{Modern Applied Statistics with S-PLUS.} Third - Edition. Springer. + Venables, W. N. and Ripley, B. D. (2002) + \emph{Modern Applied Statistics with S-PLUS.} Fourth Edition. Springer. } \seealso{ \code{\link{cov}}, \code{\link{cov.wt}}, \code{\link{cov.mve}} diff -pruN 7.3-57-1/man/drivers.Rd 7.3-58.1-1/man/drivers.Rd --- 7.3-57-1/man/drivers.Rd 2012-05-15 23:17:48.000000000 +0000 +++ 7.3-58.1-1/man/drivers.Rd 2022-07-11 11:15:20.000000000 +0000 @@ -20,8 +20,7 @@ drivers Cambridge University Press, pp. 519--523. } \references{ - Venables, W. N. and Ripley, B. D. (1999) - \emph{Modern Applied Statistics with S-PLUS.} Third - Edition. Springer. + Venables, W. N. and Ripley, B. D. (2002) + \emph{Modern Applied Statistics with S-PLUS.} Fourth Edition. Springer. } \keyword{datasets} diff -pruN 7.3-57-1/man/eagles.Rd 7.3-58.1-1/man/eagles.Rd --- 7.3-57-1/man/eagles.Rd 2012-05-15 23:17:48.000000000 +0000 +++ 7.3-58.1-1/man/eagles.Rd 2022-07-11 11:15:41.000000000 +0000 @@ -41,9 +41,8 @@ eagles \emph{Ecology} \bold{69}, 1188--1194. } \references{ - Venables, W. N. and Ripley, B. D. (1999) - \emph{Modern Applied Statistics with S-PLUS.} Third - Edition. Springer. + Venables, W. N. and Ripley, B. D. (2002) + \emph{Modern Applied Statistics with S-PLUS.} Fourth Edition. Springer. } \examples{ eagles.glm <- glm(cbind(y, n - y) ~ P*A + V, data = eagles, diff -pruN 7.3-57-1/man/genotype.Rd 7.3-58.1-1/man/genotype.Rd --- 7.3-57-1/man/genotype.Rd 2012-05-15 23:17:48.000000000 +0000 +++ 7.3-58.1-1/man/genotype.Rd 2022-07-11 11:15:58.000000000 +0000 @@ -38,8 +38,7 @@ genotype Unpublished Ph.D. thesis, University of California. Table B of the Appendix. } \references{ - Venables, W. N. and Ripley, B. D. (1999) - \emph{Modern Applied Statistics with S-PLUS.} Third - Edition. Springer. + Venables, W. N. and Ripley, B. D. (2002) + \emph{Modern Applied Statistics with S-PLUS.} Fourth Edition. Springer. } \keyword{datasets} diff -pruN 7.3-57-1/man/ginv.Rd 7.3-58.1-1/man/ginv.Rd --- 7.3-57-1/man/ginv.Rd 2018-10-16 10:08:32.000000000 +0000 +++ 7.3-58.1-1/man/ginv.Rd 2022-07-11 11:16:29.000000000 +0000 @@ -1,5 +1,5 @@ % file MASS/man/ginv.Rd -% copyright (C) 1994-2018 W. N. Venables and B. D. Ripley +% copyright (C) 1994-2022 W. N. Venables and B. D. Ripley % \name{ginv} \alias{ginv} @@ -24,9 +24,8 @@ A relative tolerance to detect zero sing A MP generalized inverse matrix for \code{X}. } \references{ - Venables, W. N. and Ripley, B. D. (1999) - \emph{Modern Applied Statistics with S-PLUS.} Third - Edition. Springer. p.100. + Venables, W. N. and Ripley, B. D. (2002) + \emph{Modern Applied Statistics with S-PLUS.} Fourth Edition. Springer. } \seealso{ \code{\link{solve}}, \code{\link{svd}}, \code{\link{eigen}} diff -pruN 7.3-57-1/man/glmmPQL.Rd 7.3-58.1-1/man/glmmPQL.Rd --- 7.3-57-1/man/glmmPQL.Rd 2022-03-22 19:49:12.000000000 +0000 +++ 7.3-58.1-1/man/glmmPQL.Rd 2022-07-27 05:24:19.000000000 +0000 @@ -1,11 +1,11 @@ \name{glmmPQL} \alias{glmmPQL} \title{ -Fit Generalized Linear Mixed Models via PQL + Fit Generalized Linear Mixed Models via PQL } \description{ -Fit a GLMM model with multivariate normal random effects, using -Penalized Quasi-Likelihood. + Fit a GLMM model with multivariate normal random effects, using + Penalized Quasi-Likelihood. } \usage{ glmmPQL(fixed, random, family, data, correlation, weights, @@ -45,38 +45,52 @@ logical: print out record of iterations? Further arguments for \code{lme}. }} \value{ -A object of class \code{"lme"}: see \code{\link[nlme]{lmeObject}}. + A object of class \code{c("glmmPQL", "lme")}: see \code{\link[nlme]{lmeObject}}. } \details{ \code{glmmPQL} works by repeated calls to \code{\link[nlme]{lme}}, so - package \code{nlme} will be loaded at first use if necessary. + namespace \CRANpkg{nlme} will be loaded at first use. (Before 2015 it + used to attach \code{nlme} but nowadays only loads the namespace.) + + Unlike \code{lme}, \code{\link{offset}} terms are allowed in + \code{fixed} -- this is done by pre- and post-processing the calls to + \code{lme}. + + Note that the returned object inherits from class \code{"lme"} and + that most generics will use the method for that class. As from + version 3.1-158, the fitted values have any offset included, as do + the results of calling \code{\link{predict}}. } \references{ -Schall, R. (1991) Estimation in generalized linear models with -random effects. -\emph{Biometrika} -\bold{78}, 719--727. - -Breslow, N. E. and Clayton, D. G. (1993) Approximate inference in -generalized linear mixed models. -\emph{Journal of the American Statistical Association} -\bold{88}, 9--25. - -Wolfinger, R. and O'Connell, M. (1993) Generalized linear mixed models: a -pseudo-likelihood approach. -\emph{Journal of Statistical Computation and Simulation} -\bold{48}, 233--243. + Schall, R. (1991) Estimation in generalized linear models with + random effects. + \emph{Biometrika} + \bold{78}, 719--727. + + Breslow, N. E. and Clayton, D. G. (1993) Approximate inference in + generalized linear mixed models. + \emph{Journal of the American Statistical Association} + \bold{88}, 9--25. + + Wolfinger, R. and O'Connell, M. (1993) Generalized linear mixed models: a + pseudo-likelihood approach. + \emph{Journal of Statistical Computation and Simulation} + \bold{48}, 233--243. Venables, W. N. and Ripley, B. D. (2002) \emph{Modern Applied Statistics with S.} Fourth edition. Springer. - } \seealso{ \code{\link[nlme]{lme}} } \examples{ -library(nlme) # will be loaded automatically if omitted summary(glmmPQL(y ~ trt + I(week > 2), random = ~ 1 | ID, family = binomial, data = bacteria)) + +## an example of an offset: the coefficient of 'week' changes by one. +summary(glmmPQL(y ~ trt + week, random = ~ 1 | ID, + family = binomial, data = bacteria)) +summary(glmmPQL(y ~ trt + week + offset(week), random = ~ 1 | ID, + family = binomial, data = bacteria)) } \keyword{models} diff -pruN 7.3-57-1/man/immer.Rd 7.3-58.1-1/man/immer.Rd --- 7.3-57-1/man/immer.Rd 2012-05-15 23:17:48.000000000 +0000 +++ 7.3-58.1-1/man/immer.Rd 2022-07-11 11:10:42.000000000 +0000 @@ -1,5 +1,5 @@ % file MASS/man/immer.Rd -% copyright (C) 1994-9 W. N. Venables and B. D. Ripley +% copyright (C) 1994-2022 W. N. Venables and B. D. Ripley % \name{immer} \alias{immer} @@ -41,9 +41,8 @@ immer \emph{The Design of Experiments.} 4th edition. Edinburgh: Oliver and Boyd. } \references{ - Venables, W. N. and Ripley, B. D. (1999) - \emph{Modern Applied Statistics with S-PLUS.} Third - Edition. Springer. + Venables, W. N. and Ripley, B. D. (2002) + \emph{Modern Applied Statistics with S-PLUS.} Fourth Edition. Springer. } \examples{ immer.aov <- aov(cbind(Y1,Y2) ~ Loc + Var, data = immer) diff -pruN 7.3-57-1/man/Insurance.Rd 7.3-58.1-1/man/Insurance.Rd --- 7.3-57-1/man/Insurance.Rd 2012-05-15 23:17:48.000000000 +0000 +++ 7.3-58.1-1/man/Insurance.Rd 2022-07-11 11:19:29.000000000 +0000 @@ -48,9 +48,8 @@ Insurance Oxford University Press. } \references{ - Venables, W. N. and Ripley, B. D. (1999) - \emph{Modern Applied Statistics with S-PLUS.} Third - Edition. Springer. + Venables, W. N. and Ripley, B. D. (2002) + \emph{Modern Applied Statistics with S-PLUS.} Fourth Edition. Springer. } \examples{ ## main-effects fit as Poisson GLM with offset diff -pruN 7.3-57-1/man/mammals.Rd 7.3-58.1-1/man/mammals.Rd --- 7.3-57-1/man/mammals.Rd 2012-05-15 23:17:48.000000000 +0000 +++ 7.3-58.1-1/man/mammals.Rd 2022-07-11 11:16:50.000000000 +0000 @@ -38,8 +38,7 @@ mammals \emph{Science} \bold{194}, 732--734. } \references{ - Venables, W. N. and Ripley, B. D. (1999) - \emph{Modern Applied Statistics with S-PLUS.} Third - Edition. Springer. + Venables, W. N. and Ripley, B. D. (2002) + \emph{Modern Applied Statistics with S-PLUS.} Fourth Edition. Springer. } \keyword{datasets} diff -pruN 7.3-57-1/man/mcycle.Rd 7.3-58.1-1/man/mcycle.Rd --- 7.3-57-1/man/mcycle.Rd 2012-05-15 23:17:48.000000000 +0000 +++ 7.3-58.1-1/man/mcycle.Rd 2022-07-11 11:17:06.000000000 +0000 @@ -29,8 +29,7 @@ mcycle \emph{Journal of the Royal Statistical Society series B} \bold{47}, 1--52. } \references{ - Venables, W. N. and Ripley, B. D. (1999) - \emph{Modern Applied Statistics with S-PLUS.} Third - Edition. Springer. + Venables, W. N. and Ripley, B. D. (2002) + \emph{Modern Applied Statistics with S-PLUS.} Fourth Edition. Springer. } \keyword{datasets} diff -pruN 7.3-57-1/man/negative.binomial.Rd 7.3-58.1-1/man/negative.binomial.Rd --- 7.3-57-1/man/negative.binomial.Rd 2012-05-15 23:17:48.000000000 +0000 +++ 7.3-58.1-1/man/negative.binomial.Rd 2022-07-11 11:17:25.000000000 +0000 @@ -34,9 +34,8 @@ negative.binomial(theta = stop("'theta' \code{\link{summary.negbin}} } \references{ - Venables, W. N. and Ripley, B. D. (1999) - \emph{Modern Applied Statistics with S-PLUS.} Third - Edition. Springer. + Venables, W. N. and Ripley, B. D. (2002) + \emph{Modern Applied Statistics with S-PLUS.} Fourth Edition. Springer. } \examples{ # Fitting a Negative Binomial model to the quine data diff -pruN 7.3-57-1/man/Rubber.Rd 7.3-58.1-1/man/Rubber.Rd --- 7.3-57-1/man/Rubber.Rd 2012-05-15 23:17:48.000000000 +0000 +++ 7.3-58.1-1/man/Rubber.Rd 2022-07-11 11:18:35.000000000 +0000 @@ -35,8 +35,7 @@ Rubber 4th edition, Longmans, Table 8.1 p. 239. } \references{ - Venables, W. N. and Ripley, B. D. (1999) - \emph{Modern Applied Statistics with S-PLUS.} Third - Edition. Springer. + Venables, W. N. and Ripley, B. D. (2002) + \emph{Modern Applied Statistics with S-PLUS.} Fourth Edition. Springer. } \keyword{datasets} diff -pruN 7.3-57-1/man/snails.Rd 7.3-58.1-1/man/snails.Rd --- 7.3-57-1/man/snails.Rd 2012-05-15 23:17:48.000000000 +0000 +++ 7.3-58.1-1/man/snails.Rd 2022-07-11 11:18:19.000000000 +0000 @@ -50,8 +50,7 @@ snails Zoology Department, The University of Adelaide. } \references{ - Venables, W. N. and Ripley, B. D. (1999) - \emph{Modern Applied Statistics with S-PLUS.} Third - Edition. Springer. + Venables, W. N. and Ripley, B. D. (2002) + \emph{Modern Applied Statistics with S-PLUS.} Fourth Edition. Springer. } \keyword{datasets} diff -pruN 7.3-57-1/man/steam.Rd 7.3-58.1-1/man/steam.Rd --- 7.3-57-1/man/steam.Rd 2012-05-15 23:17:48.000000000 +0000 +++ 7.3-58.1-1/man/steam.Rd 2022-07-11 11:17:50.000000000 +0000 @@ -28,8 +28,7 @@ steam \emph{Applied Regression Analysis.} Wiley, pp. 518--9. } \references{ - Venables, W. N. and Ripley, B. D. (1999) - \emph{Modern Applied Statistics with S-PLUS.} Third - Edition. Springer. + Venables, W. N. and Ripley, B. D. (2002) + \emph{Modern Applied Statistics with S-PLUS.} Fourth Edition. Springer. } \keyword{datasets} diff -pruN 7.3-57-1/man/survey.Rd 7.3-58.1-1/man/survey.Rd --- 7.3-57-1/man/survey.Rd 2012-05-15 23:17:48.000000000 +0000 +++ 7.3-58.1-1/man/survey.Rd 2022-07-11 11:10:05.000000000 +0000 @@ -1,5 +1,5 @@ % file MASS/man/survey.Rd -% copyright (C) 1994-9 W. N. Venables and B. D. Ripley +% copyright (C) 1994-2022 W. N. Venables and B. D. Ripley % \name{survey} \alias{survey} @@ -63,7 +63,7 @@ survey } } \references{ - Venables, W. N. and Ripley, B. D. (1999) - \emph{Modern Applied Statistics with S-PLUS.} Third Edition. Springer. + Venables, W. N. and Ripley, B. D. (2002) + \emph{Modern Applied Statistics with S-PLUS.} Fourth Edition. Springer. } \keyword{datasets} diff -pruN 7.3-57-1/man/Traffic.Rd 7.3-58.1-1/man/Traffic.Rd --- 7.3-57-1/man/Traffic.Rd 2012-05-15 23:17:48.000000000 +0000 +++ 7.3-58.1-1/man/Traffic.Rd 2022-07-11 11:12:50.000000000 +0000 @@ -41,8 +41,7 @@ Traffic \emph{Annals of Statistics,} \bold{9}, 697--704. } \references{ - Venables, W. N. and Ripley, B. D. (1999) - \emph{Modern Applied Statistics with S-PLUS.} Third - Edition. Springer. + Venables, W. N. and Ripley, B. D. (2002) + \emph{Modern Applied Statistics with S-PLUS.} Fourth Edition. Springer. } \keyword{datasets} diff -pruN 7.3-57-1/man/UScereal.Rd 7.3-58.1-1/man/UScereal.Rd --- 7.3-57-1/man/UScereal.Rd 2012-05-15 23:17:48.000000000 +0000 +++ 7.3-58.1-1/man/UScereal.Rd 2022-07-11 11:13:10.000000000 +0000 @@ -59,8 +59,7 @@ UScereal \url{http://lib.stat.cmu.edu/datasets/1993.expo/}. } \references{ - Venables, W. N. and Ripley, B. D. (1999) - \emph{Modern Applied Statistics with S-PLUS.} Third - Edition. Springer. + Venables, W. N. and Ripley, B. D. (2002) + \emph{Modern Applied Statistics with S-PLUS.} Fourth Edition. Springer. } \keyword{datasets} diff -pruN 7.3-57-1/man/UScrime.Rd 7.3-58.1-1/man/UScrime.Rd --- 7.3-57-1/man/UScrime.Rd 2012-05-15 23:17:48.000000000 +0000 +++ 7.3-58.1-1/man/UScrime.Rd 2022-07-11 11:13:29.000000000 +0000 @@ -79,8 +79,7 @@ UScrime US National Academy of Sciences. } \references{ - Venables, W. N. and Ripley, B. D. (1999) - \emph{Modern Applied Statistics with S-PLUS.} Third - Edition. Springer. + Venables, W. N. and Ripley, B. D. (2002) + \emph{Modern Applied Statistics with S-PLUS.} Fourth Edition. Springer. } \keyword{datasets} diff -pruN 7.3-57-1/MD5 7.3-58.1-1/MD5 --- 7.3-57-1/MD5 2022-04-22 11:45:27.000000000 +0000 +++ 7.3-58.1-1/MD5 2022-08-03 15:06:59.000000000 +0000 @@ -1,7 +1,8 @@ -37e8e45658ca2512e47990c80e3fe867 *DESCRIPTION +016d1fff541af35c1be2f1f9b2bab69b *ChangeLog +3feb31992fd16f6f1516af268bf95cca *DESCRIPTION 35aff05a505ecf7e81e0473767794ca9 *INDEX c7acdc0fa828f781a0a5586ab9d4fa1b *LICENCE.note -3c2dfc5f75d8a5a108ce9a1948aaf8dc *NAMESPACE +3058570082fa395ff650dacb82f17442 *NAMESPACE aed71ed40bb9bfdd7d19edfdbd163087 *R/add.R 667178114b2cc60142fed7fc16c00f90 *R/area.R 2b449dd3fde83489799ef5f72bc8ead0 *R/boxcox.R @@ -15,7 +16,7 @@ bca9a041d73f25376018c9e4cca65922 *R/cov. 81f2b80d082acd4bf2cdcdf581277cc1 *R/fitdistr.R deb0581428073be21384b2fea27457cc *R/fractions.R fdd720ed0d234e62ec46ad80ffc5c3f6 *R/gamma.shape.R -51280f00f8f92b878f6c29bf9d2d9854 *R/glmmPQL.R +c801774ec1f9e41060eec9bad3417504 *R/glmmPQL.R f6c250dc2c0287a0d9a7e577352bc3f1 *R/hist.scott.R 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*tests/polr.R +274e2255e4054f8a5adf5c0d9035d3a0 *tests/polr.R f4e6b3ffb6521ea7625515e2f0ae7f98 *tests/profile.R a23ddf89e02a02ed030e4ed5538d3430 *tests/regression.R 51c912fb8fac4844110b52651f79a8e8 *tests/regression.Rout.save f2eeba77216158f02085ec4f29e586c0 *tests/rlm.R -f5fd08eb22747dbe31443bc3560cfa2d *tests/scripts.R +0ed8f9c655ec870a37a89a759e40061f *tests/scripts.R +83342e7163a9298e6944b17eb3bcab36 *tests/solr.rda diff -pruN 7.3-57-1/NAMESPACE 7.3-58.1-1/NAMESPACE --- 7.3-57-1/NAMESPACE 2022-03-25 16:36:42.000000000 +0000 +++ 7.3-58.1-1/NAMESPACE 2022-07-05 12:12:54.000000000 +0000 @@ -38,7 +38,6 @@ export(cov.mcd, cov.mve, cov.rob, lmsreg importFrom(grDevices, dev.flush, dev.hold, nclass.FD, nclass.scott, palette) importFrom(graphics, abline, axis, box, frame, hist, lines, matplot, mtext, pairs, par, plot, points, rect, segments, symbols, text) -#import(stats) # triggers bug in wmtsa importFrom(stats, add1, anova, biplot, coef, confint, drop1, extractAIC, family, fitted, logLik, model.frame, nobs, predict, profile, residuals, se.contrast, simulate, terms, @@ -56,7 +55,9 @@ importFrom(stats, add1, anova, biplot, c napredict, naprint, naresid, optim, optimize, pcauchy, pchisq, pf, plogis, pnorm, qchisq, qf, qnorm, qt, quantile, rcauchy, rexp, rgamma, rlogis, rnorm, rpois, runif, sd, - spline, summary.glm, uniroot, update.formula, var) + spline, summary.glm, uniroot, update.formula, var, + ## added in 7.3-58 + drop.terms, reformulate) S3method("[", fractions) S3method("[<-", fractions) diff -pruN 7.3-57-1/R/glmmPQL.R 7.3-58.1-1/R/glmmPQL.R --- 7.3-57-1/R/glmmPQL.R 2022-03-25 16:36:03.000000000 +0000 +++ 7.3-58.1-1/R/glmmPQL.R 2022-07-27 05:04:17.000000000 +0000 @@ -32,14 +32,17 @@ glmmPQL <- function(fixed, random, famil for(i in nm[!keep]) m[[i]] <- NULL allvars <- if (is.list(random)) - allvars <- c(all.vars(fixed), names(random), - unlist(lapply(random, function(x) all.vars(formula(x))))) + c(all.vars(fixed), names(random), + unlist(lapply(random, function(x) all.vars(formula(x))))) else c(all.vars(fixed), all.vars(random)) ## allvars does not contain offset term. Terms <- if(missing(data)) terms(fixed) else terms(fixed, data = data) - off <- attr(Terms, "offset") - if(length(off<- attr(Terms, "offset"))) allvars <- - c(allvars, as.character(attr(Terms, "variables"))[off+1]) + offt <- attr(Terms, "offset") + have_offset <- length(offt) >= 1L + if(have_offset) { + offvars <- as.character(attr(Terms, "variables"))[offt + 1L] + allvars <- c(allvars, offvars) + } ## add variables in correlation argument, if any if (!missing(correlation) && !is.null(attr(correlation,"formula"))) allvars <- c(allvars, all.vars(attr(correlation,"formula"))) @@ -52,10 +55,19 @@ glmmPQL <- function(fixed, random, famil mf <- eval.parent(m) off <- model.offset(mf) if(is.null(off)) off <- 0 + ## as from 2022-04, nlme refuses fixed with offsets, + ## rather than ignoring them. + fixed2 <- + if(have_offset) { + tf <- drop.terms(Terms, offt, keep.response = TRUE) + reformulate(attr(tf,"term.labels"), response = fixed[[2L]], + intercept = attr(tf, "intercept"), + env = environment(fixed)) + } else fixed wts <- model.weights(mf) if(is.null(wts)) wts <- rep(1, nrow(mf)) mf$wts <- wts - fit0 <- glm(formula=fixed, family=family, data=mf, weights = wts, ...) + fit0 <- glm(formula = fixed, family = family, data = mf, weights = wts, ...) w <- fit0$prior.weights eta <- fit0$linear.predictors zz <- eta + fit0$residuals - off @@ -66,8 +78,8 @@ glmmPQL <- function(fixed, random, famil keep <- is.element(nm, c("fixed", "random", "data", "subset", "na.action", "control")) for(i in nm[!keep]) mcall[[i]] <- NULL - fixed[[2L]] <- quote(zz) - mcall[["fixed"]] <- fixed + fixed2[[2L]] <- quote(zz) + mcall[["fixed"]] <- fixed2 mcall[[1L]] <- quote(nlme::lme) mcall$random <- random mcall$method <- "ML" @@ -96,6 +108,13 @@ glmmPQL <- function(fixed, random, famil fit$call <- Call fit$family <- family fit$logLik <- as.numeric(NA) + if(have_offset) { + ## fit$fitted is a matrix + fit$fitted <- fit$fitted + off # will recycle + fit$have_offset <- TRUE + fit$fixed2 <- fixed2 + fit$offvars <- offvars + } oldClass(fit) <- c("glmmPQL", oldClass(fit)) fit } @@ -105,7 +124,7 @@ predict.glmmPQL <- level = Q, na.action = na.pass, ...) { type <- match.arg(type) - Q <- object$dims$Q + Q <- object$dims$Q # default for level if(missing(newdata)) { pred <- fitted(object, level = level) pred <- switch(type, @@ -114,9 +133,22 @@ predict.glmmPQL <- if(!is.null(object$na.action)) pred <- napredict(object$na.action, pred) } else { - class(object) <- class(object)[-1L] - pred <- predict(object, newdata, level = level, - na.action = na.action) + have_offset <- isTRUE(object$have_offset) + class(object) <- class(object)[-1L] # call lme method + if(have_offset) { + ## remove offset(s) from call + mcall <- object$call + mcall[["fixed"]] <- object$fixed2 + object$call <- mcall + pred <- predict(object, newdata, level = level, + na.action = na.action) + ## Now add back offset(s) + offvars <- sub("offset[(]", "", object$offvars) + offvars <- sub("[)]", "", offvars) + for (n in offvars) pred <- pred + eval(as.name(n), newdata) + } else + pred <- predict(object, newdata, level = level, + na.action = na.action) switch(type, response = {pred <- object$family$linkinv(pred)}, link =) diff -pruN 7.3-57-1/src/lqs.c 7.3-58.1-1/src/lqs.c --- 7.3-57-1/src/lqs.c 2022-04-11 10:02:39.000000000 +0000 +++ 7.3-58.1-1/src/lqs.c 2022-04-22 17:01:31.000000000 +0000 @@ -72,11 +72,13 @@ static void sample_noreplace(int *x, int /* Find all subsets of size k of n in order: this gets a new one each call */ -// mis-compiled by GCC 11.[012] at -O3, so avoid it. +// mis-compiled by GCC 11.[012] at -O3, so avoid it. 11.3 should be OK. // also GCC pre-12 at -O2 only up to Apr 2022 so releases should be OK. -#if defined __GNUC__ && __GNUC__ == 12 && __GNUC_MINOR__ < 1 +// clang defines __GNUC__ but not these pragmas, +// AND uses its version (LLVM or Apple) for __GNUC__ +#if !defined __clang__ && defined __GNUC__ && __GNUC__ == 12 && __GNUC_MINOR__ < 1 #pragma GCC optimize "-O1" -#elif defined __GNUC__ && __GNUC__ == 11 && __GNUC_MINOR__ <= 2 +#elif !defined __clang__ && defined __GNUC__ && __GNUC__ == 11 && __GNUC_MINOR__ <= 2 #pragma GCC optimize "-O2" #endif static void next_set(int *x, int n, int k) @@ -86,7 +88,7 @@ static void next_set(int *x, int n, int while(j > 0 && x[j] >= n - (k - 1 -j)) tmp = ++x[--j]; for(int i = j + 1; i < k; i++) x[i] = ++tmp; } -#if defined __GNUC__ +#if !defined __clang__ && defined __GNUC__ #pragma GCC reset_options #endif diff -pruN 7.3-57-1/src/MASS.c 7.3-58.1-1/src/MASS.c --- 7.3-57-1/src/MASS.c 2022-01-12 16:14:30.000000000 +0000 +++ 7.3-58.1-1/src/MASS.c 2022-07-06 13:54:15.000000000 +0000 @@ -18,6 +18,7 @@ #include #include #include +#include // for INT_MAX #include #include @@ -34,8 +35,8 @@ */ void -VR_sammon(double *dd, Sint *nn, Sint *kd, double *Y, Sint *niter, - double *stress, Sint *trace, double *aa, double *tol) +VR_sammon(double *dd, int *nn, int *kd, double *Y, int *niter, + double *stress, int *trace, double *aa, double *tol) { int i, j, k, m, n = *nn, nd = *kd; double *xu, *xv, *e1, *e2; @@ -165,11 +166,11 @@ CORRECT: * */ -static Sint *ord; /* ranks of dissimilarities */ -static Sint *ord2; /* inverse ordering (which one is rank i?) */ -static Sint n; /* number of dissimilarities */ -static Sint nr; /* number of data points */ -static Sint nc; /* # cols of fitted configuration */ +static int *ord; /* ranks of dissimilarities */ +static int *ord2; /* inverse ordering (which one is rank i?) */ +static int n; /* number of dissimilarities */ +static int nr; /* number of data points */ +static int nc; /* # cols of fitted configuration */ static int dimx; /* Size of configuration array */ static double *x; /* configuration */ static double *d; /* dissimilarities */ @@ -178,15 +179,15 @@ static double *yf; /* isotonic regressi static double mink_pow; void -VR_mds_fn(double *, double *, Sint *, double *, Sint *, - double *, Sint *, Sint *, double *, Sint *, double *); +VR_mds_fn(double *, double *, int *, double *, int *, + double *, int *, int *, double *, int *, double *); /* * Download the data. */ void -VR_mds_init_data(Sint *pn, Sint *pc, Sint *pr, Sint *orde, - Sint *ordee, double *xx, double *p) +VR_mds_init_data(int *pn, int *pc, int *pr, int *orde, + int *ordee, double *xx, double *p) { int i; @@ -194,8 +195,8 @@ VR_mds_init_data(Sint *pn, Sint *pc, Sin nr = *pr; nc = *pc; dimx = nr * nc; - ord = R_Calloc(n, Sint); - ord2 = R_Calloc(n, Sint); + ord = R_Calloc(n, int); + ord2 = R_Calloc(n, int); x = R_Calloc(dimx, double); d = R_Calloc(n, double); y = R_Calloc(n, double); @@ -237,7 +238,7 @@ static double fminfn(int nn, double *x, void *dummy) { double ssq; - Sint do_derivatives = 0; + int do_derivatives = 0; calc_dist(x); VR_mds_fn(y, yf, &n, &ssq, ord2, x, &nr, &nc, 0, &do_derivatives, @@ -249,7 +250,7 @@ static void fmingr(int nn, double *x, double *der, void *dummy) { double ssq; - Sint do_derivatives = 1; + int do_derivatives = 1; calc_dist(x); VR_mds_fn(y, yf, &n, &ssq, ord2, x, &nr, &nc, der, &do_derivatives, @@ -260,7 +261,7 @@ fmingr(int nn, double *x, double *der, v #define REPORT 5 void -VR_mds_dovm(double *val, Sint *maxit, Sint *trace, double *xx, double *tol) +VR_mds_dovm(double *val, int *maxit, int *trace, double *xx, double *tol) { int i, ifail, fncount, grcount, *mask; @@ -277,9 +278,9 @@ VR_mds_dovm(double *val, Sint *maxit, Si */ void -VR_mds_fn(double *y, double *yf, Sint *pn, double *pssq, Sint *pd, - double *x, Sint *pr, Sint *pncol, double *der, - Sint *do_derivatives, double *p) +VR_mds_fn(double *y, double *yf, int *pn, double *pssq, int *pd, + double *x, int *pr, int *pncol, double *der, + int *do_derivatives, double *p) { int n = *pn, i, ip=0, known, u, s, r = *pr, ncol = *pncol, k=0; double tmp, tmp1, sgn, ssq, *yc, slope, tstar, sstar, mink = *p; @@ -353,10 +354,10 @@ VR_mds_fn(double *y, double *yf, Sint *p /* Formulae (6.67) and (6.69) of Scott (1992), the latter corrected. */ void -VR_ucv_bin(Sint *n, Sint *nb, Sfloat *d, Sint *x, Sfloat *h, Sfloat *u) +VR_ucv_bin(int *n, int *nb, double *d, int *x, double *h, double *u) { int i, nn = *n, nbin = *nb; - Sfloat delta, hh = (*h) / 4, sum, term; + double delta, hh = (*h) / 4, sum, term; sum = 0.0; for (i = 0; i < nbin; i++) { @@ -370,10 +371,10 @@ VR_ucv_bin(Sint *n, Sint *nb, Sfloat *d, } void -VR_bcv_bin(Sint *n, Sint *nb, Sfloat *d, Sint *x, Sfloat *h, Sfloat *u) +VR_bcv_bin(int *n, int *nb, double *d, int *x, double *h, double *u) { int i, nn = *n, nbin = *nb; - Sfloat delta, hh = (*h) / 4, sum, term; + double delta, hh = (*h) / 4, sum, term; sum = 0.0; for (i = 0; i < nbin; i++) { @@ -388,10 +389,10 @@ VR_bcv_bin(Sint *n, Sint *nb, Sfloat *d, void -VR_phi4_bin(Sint *n, Sint *nb, Sfloat *d, Sint *x, Sfloat *h, Sfloat *u) +VR_phi4_bin(int *n, int *nb, double *d, int *x, double *h, double *u) { int i, nn = *n, nbin = *nb; - Sfloat delta, sum, term; + double delta, sum, term; sum = 0.0; for (i = 0; i < nbin; i++) { @@ -406,10 +407,10 @@ VR_phi4_bin(Sint *n, Sint *nb, Sfloat *d } void -VR_phi6_bin(Sint *n, Sint *nb, Sfloat *d, Sint *x, Sfloat *h, Sfloat *u) +VR_phi6_bin(int *n, int *nb, double *d, int *x, double *h, double *u) { int i, nn = *n, nbin = *nb; - Sfloat delta, sum, term; + double delta, sum, term; sum = 0.0; for (i = 0; i < nbin; i++) { @@ -425,10 +426,10 @@ VR_phi6_bin(Sint *n, Sint *nb, Sfloat *d } void -VR_den_bin(Sint *n, Sint *nb, Sfloat *d, Sfloat *x, Sint *cnt) +VR_den_bin(int *n, int *nb, double *d, double *x, int *cnt) { int i, j, ii, jj, iij, nn = *n; - Sfloat xmin, xmax, rang, dd; + double xmin, xmax, rang, dd; for (i = 0; i < *nb; i++) cnt[i] = 0; xmin = xmax = x[0]; diff -pruN 7.3-57-1/tests/confint.R 7.3-58.1-1/tests/confint.R --- 7.3-57-1/tests/confint.R 2012-05-15 23:17:47.000000000 +0000 +++ 7.3-58.1-1/tests/confint.R 2022-07-09 12:51:31.000000000 +0000 @@ -1,4 +1,5 @@ library(MASS) +pdf("confint.pdf") PropCI <- function(x, n, conf = 0.95) { diff -pruN 7.3-57-1/tests/Examples/MASS-Ex.Rout.save 7.3-58.1-1/tests/Examples/MASS-Ex.Rout.save --- 7.3-57-1/tests/Examples/MASS-Ex.Rout.save 2022-04-16 16:17:23.000000000 +0000 +++ 7.3-58.1-1/tests/Examples/MASS-Ex.Rout.save 2022-07-05 12:10:31.000000000 +0000 @@ -1,7 +1,7 @@ -R Under development (unstable) (2022-04-16 r82193) -- "Unsuffered Consequences" +R Under development (unstable) (2022-07-05 r82545) -- "Unsuffered Consequences" Copyright (C) 2022 The R Foundation for Statistical Computing -Platform: aarch64-apple-darwin21.4.0 (64-bit) +Platform: aarch64-apple-darwin21.5.0 (64-bit) R is free software and comes with ABSOLUTELY NO WARRANTY. You are welcome to redistribute it under certain conditions. @@ -1013,11 +1013,11 @@ First canonical correlation(s): 0.446368 Row scores: blue light medium dark --0.89679252 -0.98731818 0.07530627 1.57434710 + 0.89679252 0.98731818 -0.07530627 -1.57434710 Column scores: fair red medium dark black --1.21871379 -0.52257500 -0.09414671 1.31888486 2.45176017 + 1.21871379 0.52257500 0.09414671 -1.31888486 -2.45176017 > ## IGNORE_RDIFF_END > dimnames(caith)[[2]] <- c("F", "R", "M", "D", "B") > par(mfcol=c(1,3)) @@ -1182,11 +1182,11 @@ First canonical correlation(s): 0.446368 Row scores: blue light medium dark --0.89679252 -0.98731818 0.07530627 1.57434710 + 0.89679252 0.98731818 -0.07530627 -1.57434710 Column scores: fair red medium dark black --1.21871379 -0.52257500 -0.09414671 1.31888486 2.45176017 + 1.21871379 0.52257500 0.09414671 -1.31888486 -2.45176017 > biplot(corresp(caith, nf = 2)) > ## IGNORE_RDIFF_END > @@ -2216,7 +2216,6 @@ Residual Deviance: 50.09 AIC: 215.9 > > ### ** Examples > -> library(nlme) # will be loaded automatically if omitted > summary(glmmPQL(y ~ trt + I(week > 2), random = ~ 1 | ID, + family = binomial, data = bacteria)) iteration 1 @@ -2257,12 +2256,89 @@ Standardized Within-Group Residuals: Number of Observations: 220 Number of Groups: 50 > +> ## an example of an offset: the coefficient of 'week' changes by one. +> summary(glmmPQL(y ~ trt + week, random = ~ 1 | ID, ++ family = binomial, data = bacteria)) +iteration 1 +iteration 2 +iteration 3 +iteration 4 +iteration 5 +iteration 6 +Linear mixed-effects model fit by maximum likelihood + Data: bacteria + AIC BIC logLik + NA NA NA + +Random effects: + Formula: ~1 | ID + (Intercept) Residual +StdDev: 1.325243 0.7903088 + +Variance function: + Structure: fixed weights + Formula: ~invwt +Fixed effects: y ~ trt + week + Value Std.Error DF t-value p-value +(Intercept) 3.0302276 0.4791396 169 6.324310 0.0000 +trtdrug -1.2176812 0.6160113 47 -1.976719 0.0540 +trtdrug+ -0.7886376 0.6193895 47 -1.273250 0.2092 +week -0.1446463 0.0392343 169 -3.686730 0.0003 + Correlation: + (Intr) trtdrg trtdr+ +trtdrug -0.622 +trtdrug+ -0.609 0.464 +week -0.481 0.050 0.030 + +Standardized Within-Group Residuals: + Min Q1 Med Q3 Max +-4.2868074 0.2039043 0.3140333 0.5440835 1.9754065 + +Number of Observations: 220 +Number of Groups: 50 +> summary(glmmPQL(y ~ trt + week + offset(week), random = ~ 1 | ID, ++ family = binomial, data = bacteria)) +iteration 1 +iteration 2 +iteration 3 +iteration 4 +iteration 5 +iteration 6 +Linear mixed-effects model fit by maximum likelihood + Data: bacteria + AIC BIC logLik + NA NA NA + +Random effects: + Formula: ~1 | ID + (Intercept) Residual +StdDev: 1.325243 0.7903088 + +Variance function: + Structure: fixed weights + Formula: ~invwt +Fixed effects: y ~ trt + week + offset(week) + Value Std.Error DF t-value p-value +(Intercept) 3.0302276 0.4791396 169 6.324310 0.0000 +trtdrug -1.2176812 0.6160113 47 -1.976719 0.0540 +trtdrug+ -0.7886376 0.6193895 47 -1.273250 0.2092 +week -1.1446463 0.0392343 169 -29.174622 0.0000 + Correlation: + (Intr) trtdrg trtdr+ +trtdrug -0.622 +trtdrug+ -0.609 0.464 +week -0.481 0.050 0.030 + +Standardized Within-Group Residuals: + Min Q1 Med Q3 Max +-4.2868074 0.2039043 0.3140333 0.5440835 1.9754065 + +Number of Observations: 220 +Number of Groups: 50 +> > > > cleanEx() - -detaching ‘package:nlme’ - > nameEx("housing") > ### * housing > @@ -5074,7 +5150,7 @@ Achieved convergence tolerance: 4.318e-0 > cleanEx() > options(digits = 7L) > base::cat("Time elapsed: ", proc.time() - base::get("ptime", pos = 'CheckExEnv'),"\n") -Time elapsed: 2.21 0.101 2.315 0 0 +Time elapsed: 2.293 0.108 2.438 0 0 > grDevices::dev.off() null device 1 diff -pruN 7.3-57-1/tests/glmmPQL.R 7.3-58.1-1/tests/glmmPQL.R --- 7.3-57-1/tests/glmmPQL.R 1970-01-01 00:00:00.000000000 +0000 +++ 7.3-58.1-1/tests/glmmPQL.R 2022-07-27 05:27:33.000000000 +0000 @@ -0,0 +1,64 @@ +### example of glmmPQL with offset. + +### glmmPQL age structured sole egg data example +### from "GAMs:An Intro with R" by Simon Wood + +library(MASS) +if(!requireNamespace("nlme", quietly = TRUE)) q("no") + +options(warn = 2L) +## Chapter 2 stuff... + +if(FALSE) { ## script to create solr +#require(gamair) # for 'data(sole)' +data(sole) +sole$off <- log(sole$a.1 - sole$a.0) # model offset term +sole$a <-(sole$a.1 + sole$a.0)/2 # mean stage age +solr <- sole # make copy for rescaling +solr$t <- solr$t-mean(sole$t) +solr$t <- solr$t/var(sole$t)^0.5 +solr$la <- solr$la - mean(sole$la) +solr$lo <- solr$lo - mean(sole$lo) +save(solr, file = "solr.rda", version = 2) +} else load("solr.rda") + +solr$station <- factor(with(solr, paste0(-la, -lo, -t))) +b <- glmmPQL(eggs ~ offset(off) + lo + la + t + I(lo*la) + I(lo^2) + + I(la^2) + I(t^2) + I(lo*t) + I(la*t) + I(lo^3) + I(la^3) + + I(t^3) + I(lo*la*t) + I(lo^2*la) + I(lo*la^2) + I(lo^2*t) + + I(la^2*t) + I(la*t^2) + I(lo*t^2) + a + I(a*t) + I(t^2*a), + random = list(station = ~1), + family = quasi(link = log, variance = "mu"), + data = solr) +summary(b) + +b1 <- update(b, ~ . - I(lo*la*t)) +summary(b1) + +b2 <- update(b1, ~ . - I(lo*t)) +summary(b2) + +b3 <- update(b2, ~ . - I(lo^2*t)) +summary(b3) + +b4 <- update(b3, ~ . - I(la*t^2)) +summary(b4) + +pdf("glmmPQL.pdf") +fv <- exp(fitted(b4)) # fitted values include offset from 3.1-158 +resid <- solr$eggs - fv # raw residuals +sqrt_fv <- sqrt(fv) +plot(sqrt_fv, sqrt(solr$eggs)) +abline(0, 1, lwd = 2) +plot(sqrt_fv, resid/sqrt_fv) +plot(sqrt_fv, resid) +fl <- sort(sqrt_fv) +## add 1 s.d. and 2 s.d. reference lines +lines(fl, fl); lines(fl, -fl); lines(fl, 2 * fl, lty = 2) +lines(fl, -2 * fl, lty = 2) + +nlme::intervals(b4, which = "var-cov") + +head(p1 <- predict(b)) +head(p2 <- predict(b, solr)) +all.equal(p1, p2, check.attributes = FALSE) diff -pruN 7.3-57-1/tests/polr.R 7.3-58.1-1/tests/polr.R --- 7.3-57-1/tests/polr.R 2012-10-02 10:28:35.000000000 +0000 +++ 7.3-58.1-1/tests/polr.R 2022-07-20 12:22:56.000000000 +0000 @@ -1,5 +1,7 @@ ## tests from David Firth 2004-Oct-13 +pdf("polr.pdf") + library(MASS) y <- structure(as.integer(c(1, 2, 3, 1, 2, 3)), .Label = c("1", "2", "3"), class = c("ordered", "factor")) diff -pruN 7.3-57-1/tests/scripts.R 7.3-58.1-1/tests/scripts.R --- 7.3-57-1/tests/scripts.R 2012-05-15 23:17:47.000000000 +0000 +++ 7.3-58.1-1/tests/scripts.R 2022-07-09 16:40:31.000000000 +0000 @@ -1,3 +1,7 @@ +### This requires packages not declared in Suggests (and not otherwise used) +## GLMMGibbs Kernsmooth boot e1071 fastICA gee interp lattice mda +## mgcv multcomp nlme nnet polsplin rpart spatial splines tree + if(!nzchar(Sys.getenv("MASS_TESTING"))) q("no") unlink("scripts", recursive = TRUE) dir.create("scripts") Binary files 7.3-57-1/tests/solr.rda and 7.3-58.1-1/tests/solr.rda differ