version 7.3-58

ChangeLog

@@ -1,10 +1,25 @@
-7.3-57.! (released 2022-05-30)
+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: name PDF file for confint.R
+	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 <limits.h> 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
@@ -13,11 +28,9 @@
 	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.
@@ -35,7 +48,38 @@
 	expaand description of 'data' args.
 
 7.3-52 (released 2020-08-18)
-	add it translations
 	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.

DESCRIPTION

@@ -1,11 +1,11 @@
 Package: MASS
 Priority: recommended
-Version: 7.3-57.1
-Date: 2022-05-29
-Revision: $Rev: 3579 $
+Version: 7.3-58
+Date: 2022-07-14
+Revision: $Rev: 3600 $
 Depends: R (>= 3.3.0), grDevices, graphics, stats, utils
 Imports: methods
-Suggests: lattice, nlme, nnet, survival
+Suggests: lattice, nlme, nnet, survival, gamair
 Authors@R: c(person("Brian", "Ripley", role = c("aut", "cre", "cph"),
                     email = "ripley@stats.ox.ac.uk"),
 	     person("Bill", "Venables", role = "ctb"),
@@ -24,7 +24,7 @@ License: GPL-2 | GPL-3
 URL: http://www.stats.ox.ac.uk/pub/MASS4/
 Contact: <MASS@stats.ox.ac.uk>
 NeedsCompilation: yes
-Packaged: 2022-05-30 06:43:24 UTC; ripley
+Packaged: 2022-07-14 08:27:35 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 <ripley@stats.ox.ac.uk>
 Repository: CRAN
-Date/Publication: 2022-05-30 06:46:33 UTC
+Date/Publication: 2022-07-14 10:19:17 UTC

MD5

@@ -1,8 +1,8 @@
-8575bf59f49ffa7fffd23fd26e4cbd98 *ChangeLog
-aa3fbdfe76a208eb75d290b65953a152 *DESCRIPTION
+c0b694ac4c2b71b353d528baa1a09cbc *ChangeLog
+13e3cd3652c1f446c21995e7252c94b4 *DESCRIPTION
 35aff05a505ecf7e81e0473767794ca9 *INDEX
 c7acdc0fa828f781a0a5586ab9d4fa1b *LICENCE.note
-3c2dfc5f75d8a5a108ce9a1948aaf8dc *NAMESPACE
+3058570082fa395ff650dacb82f17442 *NAMESPACE
 aed71ed40bb9bfdd7d19edfdbd163087 *R/add.R
 667178114b2cc60142fed7fc16c00f90 *R/area.R
 2b449dd3fde83489799ef5f72bc8ead0 *R/boxcox.R
@@ -16,7 +16,7 @@ bca9a041d73f25376018c9e4cca65922 *R/cov.trob.R
 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
 66ee029442522726306cd7d4a869b725 *R/huber.R
 feed05160fcb53f8d07c559e1afa9873 *R/hubers.R
@@ -47,7 +47,7 @@ f1db7f02de9bae7087fc01a7ffe4748e *R/truehist.R
 bbde4307b98d968e9b85d55f46a0cbe6 *R/ucv.R
 29fdbf836b6ebffc562ce7d2b54ab5eb *R/write.matrix.R
 4f74ab00a8fd8a8eaf56957b1e13aa52 *R/zzz.R
-1961639f6f4f7f9efffa91b624b3d060 *build/partial.rdb
+0c6ad5b3446721162c89589e8077ab1c *build/partial.rdb
 e4aa969dc4062a5dfa605a141bf32f29 *data/Aids2.rda
 3c5a57a9f86ee32ac10f6114826a762b *data/Animals.rda
 689cd33a62093be4f53a38cc8405e083 *data/Boston.rda
@@ -153,37 +153,37 @@ ea5dfb16715140492edf278a4c2cb1b6 *inst/scripts/ch06.R
 d5977faadde512bc29fd49e8d10ab80d *inst/scripts/ch08.R
 8fa4f5b6039ff3883a17226085ed77b8 *inst/scripts/ch09.R
 3c43589522f6f8cd3e338be9cc067918 *inst/scripts/ch10.R
-6d19699220b04f2400f7b2e4c90a6feb *inst/scripts/ch11.R
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 793b62dd2329642c3e5e9af5962a0f59 *inst/scripts/ch12.R
-81629a5320cd986c06164748c66e0cfa *inst/scripts/ch13.R
+ac538e49531483ef589d20da73bbabc1 *inst/scripts/ch13.R
 a7457b4533a20b3ec155fe157b2ed29c *inst/scripts/ch14.R
-caebd3270cdb7268117f8a5a0cddd7be *inst/scripts/ch15.R
+fe7caab9f9c054a1f261cafc2ac90fe0 *inst/scripts/ch15.R
 3a3a57e6adb876a749a48669092ee37b *inst/scripts/ch16.R
 1b78ed518f4fbf6ed3704b0a8463715b *man/Aids2.Rd
-d5b9cf75996ccdc90872d49b2f87cae5 *man/Animals.Rd
+254cff0c5ca4d06b2efab6ceda46e948 *man/Animals.Rd
 e0715295dbeae3214279d07bd1d89116 *man/Boston.Rd
-0ac21fa2c81d16c1e1efdb6b2ca5aea7 *man/Cars93.Rd
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 e1cc4debb9ba4982b2a78864d03bf5d7 *man/Cushings.Rd
 5e497af7fdc9b4d6b7e771f3839a0c4e *man/DDT.Rd
 fc4ebf60ca33228804e86cd08ee7b990 *man/GAGurine.Rd
-a4e54a0b5a237fcde8f47b5d82daa8b4 *man/Insurance.Rd
+fe121563de0c24631efbaffaad856cd1 *man/Insurance.Rd
 a6a2cea128307c1138bde4c046fcfb5c *man/MASS-internal.Rd
 fa8c2c8e00a52e7731604be22fafcec6 *man/Melanoma.Rd
 9535c4de30b076e0ba2ec4d1f868b9ac *man/Null.Rd
 9071e3f3ca15b70da7dfed264675d965 *man/OME.Rd
 b3ee04fa917bb291c47d52830d77ffdc *man/Pima.tr.Rd
 a7ba31f8b57db3cbb58b636ec45ad19d *man/Rabbit.Rd
-fe5a281b62e06246a5e043e441257282 *man/Rubber.Rd
+c542b9d655977d4279f267e714581841 *man/Rubber.Rd
 8f350cbf5a680ecd0eaf8bcd8934e2ad *man/SP500.Rd
 d59fb4bdaf0c58b26c3443c7c8c5af70 *man/Sitka.Rd
 4cabfa1e280f74cc87b27664d417fd5b *man/Sitka89.Rd
 c74d63d7d404fa5b71d94b8fa709432e *man/Skye.Rd
-b71d552e44d70d597229eb1360d84476 *man/Traffic.Rd
-301925fbb443e0eb6b58aca56a5457b9 *man/UScereal.Rd
-9fbe1bf1cab5a1568c87457a95b5047a *man/UScrime.Rd
+84c2befbabf2142b5372b94d57aaf02b *man/Traffic.Rd
+01ace845290cc6ce0390c3a0f5453fcd *man/UScereal.Rd
+55e272a8527baa10a1f9da76920402ae *man/UScrime.Rd
 182ebb9e30ae5ba85119ce994468e775 *man/VA.Rd
 a73f6ef91062b7bd5009144b5710de5a *man/abbey.Rd
-782206216efe4e320c87191ecdccfc73 *man/accdeaths.Rd
+63ff4eb03236a0da626c040dc88bbe09 *man/accdeaths.Rd
 7de173c292018dc9b23aa17f5f65a41b *man/addterm.Rd
 a5f53921ca9d0b1553c030db03ddfe65 *man/anorexia.Rd
 bc308c384834629fa93aca2fce82f6ff *man/anova.negbin.Rd
@@ -193,10 +193,10 @@ a81030efe33e0a82e2f9e3709b1273b9 *man/bacteria.Rd
 e79ea25d60ba827b71a57f7458f733d2 *man/bcv.Rd
 61fbfe12f436f23b478400e0c085731d *man/beav1.Rd
 9c16e1752eba19b699081c3f7f82db01 *man/beav2.Rd
-1b3cede44318f5ea8feb3c3b457bdc09 *man/biopsy.Rd
+55b0db236ec4393bae165ab49c92ee48 *man/biopsy.Rd
 2f6ba17e14d2daa4afc541d3445190ad *man/birthwt.Rd
 bebc2ad312668d479d67adbb5fd3777d *man/boxcox.Rd
-2ca64d5540ffa5e91f3c8461e6e3124b *man/cabbages.Rd
+1a1233168369b0abcf4e2d207d99dc72 *man/cabbages.Rd
 9a9a2f5323a13a701a74a514785cd771 *man/caith.Rd
 726868057d0e31cad05e01c7b379573c *man/cats.Rd
 017ddc74606e2e08885a718313f9ea6b *man/cement.Rd
@@ -207,15 +207,15 @@ e35fa2f6ee37f213648c7ec087ce8b83 *man/confint.Rd
 88bb557bbfe7f9a6889f4f01ef7f490f *man/coop.Rd
 4b5232b75977adcc4eafa9823e8d3912 *man/corresp.Rd
 7c046b9650055e52296467fbe378309a *man/cov.rob.Rd
-b1a92f03d6905de2e74059df3a93f334 *man/cov.trob.Rd
+17b3d4c8aa244294ab5f01cdf31d4559 *man/cov.trob.Rd
 795a3a88f04d699ea466dbefb30adfcf *man/cpus.Rd
 1b1a88e76542006a6df88ef82a41d1c9 *man/crabs.Rd
 f320aaa10f4cff23eff1f1414c057eae *man/deaths.Rd
 5b97a49cfb656281f09aa8ec8dd389e2 *man/denumerate.Rd
 4251dd1e5e0570095044c278b4cc2690 *man/dose.p.Rd
-c5683d0ee4538c54e29683c313cf4d20 *man/drivers.Rd
+32d46414b81cc9c21663b07a5b3e24a1 *man/drivers.Rd
 989cb309d961aca2b8d9d54df183223d *man/dropterm.Rd
-a186e33c5945178fa1ca69a433c1bf3b *man/eagles.Rd
+57e48204af505d9d279440f9a75fe46d *man/eagles.Rd
 5d544d4123e89ce9b4404630c3ae53b8 *man/epil.Rd
 df9ff3b3ed9842a6c2d767dfb14233d8 *man/eqscplot.Rd
 d6c9433b3ee2a9fe920dcedecbefdf06 *man/farms.Rd
@@ -227,19 +227,19 @@ e2971220e00d364f968079d07203da26 *man/galaxies.Rd
 a980e6f05828b7c992709a22a23a2f38 *man/gamma.dispersion.Rd
 c1c0977e3730dcc6340a845b0509dff7 *man/gamma.shape.glm.Rd
 3f1ac8a8ecc476a9b8a78d8731a76bce *man/gehan.Rd
-d705175d2d756430ab571ee1c5253118 *man/genotype.Rd
+bfea377b88c51c2483cb09fca89a7967 *man/genotype.Rd
 353d48920fe6e849fb2e0a757d277901 *man/geyser.Rd
 a81ca88a2a39298dd099c015fdd3c167 *man/gilgais.Rd
-cd1607060ff90b41e5fd22b3b058d5e9 *man/ginv.Rd
+9b36e4d9f64bd4a4629a98d709fb8752 *man/ginv.Rd
 67ac548358fe00a107e17c7101fb4552 *man/glm.convert.Rd
 68625209b126bf126b0a7cad4e6c5508 *man/glm.nb.Rd
-b4003214294743d98c209ea23eb53c19 *man/glmmPQL.Rd
+b07145bdfcdcf3d621483562aab95335 *man/glmmPQL.Rd
 e65737579ca1cd2810198d72f0260e21 *man/hills.Rd
 5440204f0acdca119adda063b91d9e17 *man/hist.scott.Rd
 4b3d83cc89b49bdbf178503b6fa33dd3 *man/housing.Rd
 3ff54e8dfc1c1b949d3a33fcbd916fee *man/huber.Rd
 7cb24fac3e55b03ac894c3be943287bf *man/hubers.Rd
-bcc1aae22252614560be9bc37fffb161 *man/immer.Rd
+606105b6a9c526833a3116619a07d9c9 *man/immer.Rd
 f5e6f603789ab4838cd41e009e0890eb *man/isoMDS.Rd
 be8257b0890c6c52c5faf72cdf1781b5 *man/kde2d.Rd
 f2aec533ce897bd9f2e53ced57697ed0 *man/lda.Rd
@@ -251,16 +251,16 @@ f509645d4aa94d7b27e4537542daad97 *man/ldahist.Rd
 82b7f4c063c79b490fe7e02d261ddbb7 *man/loglm1.Rd
 4ccf847b74d8eabfa2608f644a1a5f5c *man/logtrans.Rd
 59c78564e95b8d79447af0f21ed60bc9 *man/lqs.Rd
-2a0b5dd4c71cf01dfc1894be0e8f759b *man/mammals.Rd
+fbec6bc6908ad65e919c06945c4d6b42 *man/mammals.Rd
 9fbb7d21860ae43c710d73e78d68741f *man/mca.Rd
-2f262617ef9117ab6d2fdedcdb243913 *man/mcycle.Rd
+2ef0781ce1fcb86d8362de7d6f8b41fe *man/mcycle.Rd
 b80802b32e6e02f772806bbcf21a6ad6 *man/menarche.Rd
 cb0833e592bf5cd241499c439c69a002 *man/michelson.Rd
 f8a1e349fbe9051ba75a935ba2803149 *man/minn38.Rd
 2b7e747f5cf31f4ba254a7868773c9ba *man/motors.Rd
 6dba6358bce7917dc3262ee2dd120636 *man/muscle.Rd
 6a8457e7526c032ff7e0a42e6fdc0e09 *man/mvrnorm.Rd
-fbf5b11e7ed253d29500bac780e2e794 *man/negative.binomial.Rd
+4f4344c6079fb07aa9e9387c4f3610c9 *man/negative.binomial.Rd
 c73e2dbd1f3749c2a85df1c993699d9f *man/newcomb.Rd
 0d589532d9330eedf9abb57688afdab6 *man/nlschools.Rd
 9e1448db88f35cf2fe22a0b358514a3c *man/npk.Rd
@@ -295,16 +295,16 @@ d1d51c68168df1699f03e03c922b1a3a *man/ships.Rd
 622b42b7de01cd0d290f57a0b9086402 *man/shoes.Rd
 8e8dfdcbc8597b5bccdf2728316e73dd *man/shrimp.Rd
 ba511bdea2ec00b3962296a3b6cd7cde *man/shuttle.Rd
-6fecb36e859210cc8e28f1d71d5c3a7b *man/snails.Rd
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 751d64a2da0a7ff44cdb9a8ff520ccd8 *man/stdres.Rd
-ff7bd7ff1c80f2b1206305a051376ba0 *man/steam.Rd
+c7cfb9197843a5cbd76e866013fbcce0 *man/steam.Rd
 3220d80bbff1399f7435c48def2a7f01 *man/stepAIC.Rd
 6f7889f5e4478412a523eedaefdc91aa *man/stormer.Rd
 87595689a17d00aa5b5e98845be4ca1c *man/studres.Rd
 9120d03a6f70c2ffaf8c38ca75591429 *man/summary.loglm.Rd
 1d714038b6e5bc7641181331d095e989 *man/summary.negbin.Rd
 b70f43a1c1766f0e3dc2ed66bebabd1c *man/summary.rlm.Rd
-e68bc524ad07b0ab7cb5cdf7a53f4759 *man/survey.Rd
+156b0a165f0f7ced7f97ef8743aae7bb *man/survey.Rd
 3c044bf1596134e8329f1f9aca07b7aa *man/synth.tr.Rd
 760b565cac1dcc4db7b25f77950c71b8 *man/theta.md.Rd
 819320fb15b6ddb76e79f7f1a8f7d5c1 *man/topo.Rd
@@ -321,20 +321,21 @@ ceefe8e558dfa70a28f54fcae1ca3df0 *man/whiteside.Rd
 2f300df61a52b6d876d9ebadcc447cd2 *po/R-it.po
 1191b3abb0caad62ecd5e4ad544361c4 *po/R-ko.po
 b6e225a125d6368318896f92ffd91e0f *po/R-pl.po
-c266b9259aa82d894cae84abcdfc2c6c *src/MASS.c
+f47fd24f72996b91d2a1618cd105c908 *src/MASS.c
 2c7b72ca038d349935bcb4f60235bcd7 *src/lqs.c
 7b1360150b8598b576e82534b12345a2 *tests/BankWages.rda
-31c485d8c85fdda93c7248b83e0f1bbb *tests/Examples/MASS-Ex.Rout.save
-d87553db40364fdc9c337fa31c009b17 *tests/confint.R
+ec6ef25ee362a716d1d40d7906594ff0 *tests/Examples/MASS-Ex.Rout.save
+a309c9e287f72ae6fc239b0495d5685e *tests/confint.R
 e059b0451b55d1e8cb8ebf51ecce76ea *tests/cov.mcd.R
 a0854fee9b36691ca1d0880da31d6f79 *tests/fitdistr.R
 55c6f4de353b9479359459d2718a017e *tests/fitdistr.Rout.save
 afd4f607cba7fda8ec4d22bffd88fc50 *tests/glm.nb.R
+64092b8d225221ebd25b7176da833588 *tests/glmmPQL.R
 7fea2161b12d01c8940107342815dd0e *tests/hubers.R
 7f6efdd17aea2750feda4db0abd46d48 *tests/lme.R
 edee76adc2d27e4ba90f1ff79360148b *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

NAMESPACE

@@ -38,7 +38,6 @@ export(cov.mcd, cov.mve, cov.rob, lmsreg, lqs, lqs.formula, ltsreg)
 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, coef, confint, drop1,
            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)