@r-universe/webr 2023.6.11 → 2023.6.21

package/dist/vfs/usr/lib/R/library/stats/tests/offsets.R

@@ -0,0 +1,39 @@
+## tests of offsets, and prediction from them.
+
+load("anorexia.rda") # copied from package MASS
+
+## via formula
+fit1 <- lm(Postwt ~ Prewt + Treat + offset(Prewt), data = anorexia)
+summary(fit1)
+pred <- fitted(fit1)
+stopifnot(all.equal(predict(fit1, anorexia), pred))
+
+## via argument
+fit2 <- lm(Postwt ~ Prewt + Treat, data = anorexia, offset=Prewt)
+summary(fit2)
+stopifnot(all.equal(predict(fit2, anorexia), pred))
+
+## now split into two parts
+anorexia$o1 <- 0.9*anorexia$Prewt
+anorexia$o2 <- 0.1*anorexia$Prewt
+fit3 <- lm(Postwt ~ Prewt + Treat + offset(o1) + offset(o2), data = anorexia)
+summary(fit3)
+stopifnot(all.equal(predict(fit3, anorexia), pred))
+
+fit4 <- lm(Postwt ~ Prewt + Treat + offset(o1), data = anorexia, offset = o2)
+summary(fit4)
+stopifnot(all.equal(predict(fit4, anorexia), pred))
+
+## using more than one offset failed in R 2.8.1
+
+
+## Using variable a name starting with "(weights)" :
+anoD <- within(anorexia, `(weights)_2` <- Prewt)
+fit5 <- lm(Postwt ~ `(weights)_2` + Treat + offset(o1) + offset(o2), data = anoD)
+summary(fit5)
+stopifnot(exprs = {
+    all.equal(predict(fit5, anoD), pred)
+    all.equal(sigma(fit5), sigma(fit1))
+    is.null(model.weights(model.frame(fit5)))
+})
+## these were all (even the model fit!) wrong in R <= 4.2.1

package/dist/vfs/usr/lib/R/library/stats/tests/ppr.R

@@ -0,0 +1,6 @@
+## example from PR#13571: should fail, not crash.
+
+require("stats")
+bad <- as.matrix(read.csv("ppr_test.csv"))
+try(ppr(bad[,-3], bad[, 3], nterms=1))
+

package/dist/vfs/usr/lib/R/library/stats/tests/ppr_test.csv

@@ -0,0 +1,443 @@
+"","","bady"
+"1",-0.0348207628376986,1,-0.542937988158036
+"2",-0.0191633397482220,2,-0.169266091065016
+"3",-0.0341944659141195,1,-0.275406839429961
+"4",0.0249905933641021,2,0.384150222915368
+"5",0.0155961395104161,2,0.2341732751562
+"6",-0.0792878444118122,2,-0.021997198276666
+"7",-0.0248000120604336,1,0.399971463068032
+"8",0.108914381123697,1,-0.623493578304602
+"9",0.00620168565673016,1,-0.402266282137639
+"10",-0.034507614375909,2,1.08390058914255
+"11",-0.0905611890362353,2,0.024273472328843
+"12",0.0459715403040008,1,-0.448251018679603
+"13",-0.00976888589453599,2,0.70163011189378
+"14",-0.0157187066685371,1,0.123718062829826
+"15",-6.12835790604833e-05,2,0.0929302960910126
+"16",0.107661787276539,1,0.0445186997621552
+"17",-0.0238605666750649,2,-0.268966040102523
+"18",0.0494161733836856,1,-0.244466585236197
+"19",-0.0194764882100115,2,-0.272492268970116
+"20",-0.0113346282034837,2,0.58637312706044
+"21",-0.043275771306016,2,-0.388224863429526
+"22",-0.0263657543693812,1,-0.439522809120621
+"23",0.00776742796567782,2,-0.354209517739221
+"24",-0.0473467013092799,1,-0.166859766555732
+"25",-0.0188501912864324,2,0.265535097126863
+"26",0.0046359433477825,1,0.342255739372447
+"27",-0.0961978613484469,2,0.328193133923304
+"28",-0.0435889197678055,2,-0.738100695537103
+"29",-0.0376390989938044,2,0.0492751978645918
+"30",-0.0958847128866574,1,0.846962244613297
+"31",-0.00757684666200928,2,-0.311395214189561
+"32",-0.0536096705450705,2,-0.197180299226387
+"33",-0.0129003705124313,1,0.770727634055679
+"34",-0.0899348921126563,2,-0.214099277802346
+"35",-0.0489124436182275,2,-0.328796268354374
+"36",-0.00413221358232442,1,-0.123798883552826
+"37",-0.0285577936019079,2,0.557326881019212
+"38",-0.0429626228442264,2,0.910078165810043
+"39",0.0754074957122168,1,0.0625474905222085
+"40",0.00620168565673016,1,-0.660060421124099
+"41",0.07321545647969,1,-0.648765887241763
+"42",-0.072711726714232,2,-0.291387183530275
+"43",-0.0235474182132754,1,-0.580764200095337
+"44",-0.0100820343563255,2,-0.213881238361436
+"45",0.0046359433477825,1,0.342219498341999
+"46",0.00150445872988718,1,-0.627738756029472
+"47",-0.0476598497710694,2,0.638490421487924
+"48",-0.0742774690231797,2,0.366998080026886
+"49",0.00588853719494063,1,-0.192002931323743
+"50",0.00620168565673016,1,-0.42703489754501
+"51",-0.0373259505320149,2,0.399143495901645
+"52",-0.029184090525487,1,0.259085862758254
+"53",0.0447189464568426,2,-0.52960117919881
+"54",0.0221722572079963,2,-0.358445653831134
+"55",0.0177881787429428,2,0.299979528574020
+"56",-0.0226079728279068,2,0.34651271103047
+"57",-0.0304366843726451,2,-1.28260529016723
+"58",-0.104339721354975,2,-0.469681693832029
+"59",-0.057993749010124,2,0.572875739287276
+"60",0.048476727998317,1,0.318516539900054
+"61",-0.0786615474882331,2,-0.51629774307693
+"62",-0.0273051997547498,1,-0.238363914682604
+"63",-0.0138398158977999,1,-0.278262054849107
+"64",0.0434663526096845,2,0.240351359037258
+"65",-0.0598726397808612,1,-0.439820093575709
+"66",0.0149698425868371,1,-0.089734626673025
+"67",0.0121515064307313,1,0.157744469530662
+"68",0.00839372488925688,1,-0.147761547457720
+"69",-0.0241737151368545,1,0.640629492509571
+"70",-0.0614383820898088,2,0.721507998029808
+"71",-0.00914258897095694,2,-0.391891463942708
+"72",0.0262431872112602,2,0.409309553303869
+"73",0.0487898764601065,1,0.218024247023677
+"74",0.05317395492516,1,-0.149519213731968
+"75",0.0171618818193638,1,-0.647105867961298
+"76",-0.00100072896442909,1,-0.711807768742965
+"77",-0.106844909049291,1,-0.0568622733771722
+"78",-0.0276183482165393,2,0.95979439504761
+"79",-0.0683276482491785,2,1.05882959546064
+"80",0.0199802179754696,2,0.202513236360187
+"81",0.0534871033869495,2,-0.160509136618631
+"82",0.0284352264437869,1,-0.585827752105968
+"83",0.0171618818193638,2,-0.346456582878112
+"84",-0.0529833736214915,2,0.597901713985014
+"85",-0.0301235359108556,2,-0.132649008239744
+"86",-0.00100072896442909,2,-0.289025947256112
+"87",-0.0150924097449580,1,-0.255121884845899
+"88",0.0162224364339952,2,-0.136854078336641
+"89",-0.0370128020702253,1,-0.677430950151256
+"90",-0.0160318551303266,2,0.0753389806448792
+"91",-0.0451546620767532,2,0.100243021636830
+"92",0.0647604480113727,2,-0.125255305348025
+"93",-0.0207290820571696,2,-1.0505758255551
+"94",-0.0154055582067476,2,0.16885039497003
+"95",-0.0135266674360104,2,-0.169309597945285
+"96",-0.0288709420636975,2,0.369854431600131
+"97",-0.0122740735888523,1,-0.566282851696723
+"98",0.0425269072243159,2,0.556556637552114
+"99",-0.0138398158977999,1,-0.343832598689341
+"100",0.0375165318356834,2,-0.268130829056743
+"101",0.0444057979950531,2,-0.365938550530639
+"102",-0.00037443204085002,1,-0.0311681764689511
+"103",0.0249905933641021,2,1.22944913120819
+"104",0.0707102687853738,1,0.201090437227192
+"105",-0.0172844489774848,2,-0.594182131644277
+"106",-0.0216685274425382,1,-0.488925578404151
+"107",-0.0348207628376986,2,0.400182859035963
+"108",0.0406480164535787,2,0.0155260921851867
+"109",-0.0558017097775973,1,0.1349613580299
+"110",0.0375165318356834,1,-0.604279409412377
+"111",-0.0401442866881206,1,0.0912229513254876
+"112",0.0102726156599941,2,-0.585827187420521
+"113",0.0196670695136800,2,0.821569273382661
+"114",0.0202933664372591,1,0.779534939715196
+"115",-0.0329418720669614,2,-0.0427576052327692
+"116",0.0494161733836856,1,0.34552055454062
+"117",0.0206065148990486,1,0.627600258862538
+"118",0.0315667110616823,2,0.560348866635563
+"119",0.0400217195299996,1,0.136561803275829
+"120",-0.0429626228442264,2,0.586659396678506
+"121",-0.0185370428246429,2,0.751858555892416
+"122",0.0215459602844172,2,-0.0346520027699464
+"123",0.0641341510877936,1,-0.475034031350191
+"124",0.198787989657293,1,-0.96267443600314
+"125",-0.0388916928409625,2,-0.446966403216099
+"126",-0.0636304213223356,1,-0.105229435869263
+"127",-0.0545491159304391,2,0.111213728568517
+"128",0.0137172487396789,1,-0.225021888807548
+"129",-0.005071658967693,2,0.192382971695893
+"130",0.0105857641217836,2,0.544550640526851
+"131",-0.00475851050590347,1,0.169227048178445
+"132",-0.0107083312799046,2,0.645013058812764
+"133",0.047850431074738,1,-0.0235134031161297
+"134",-0.0717722813288634,1,-0.0630297490026158
+"135",0.000251864882729031,2,-0.371022927651655
+"136",-0.0429626228442264,2,0.481214559043027
+"137",-0.068014499787389,2,0.00232117243748586
+"138",-0.0163450035921162,2,0.603296973022765
+"139",-0.03388131745233,1,0.689463397801391
+"140",-0.0489124436182275,2,0.584785784895232
+"141",-0.00131387742621863,1,-0.362779810283891
+"142",0.0572448849284239,2,0.810287091899672
+"143",0.0444057979950531,1,0.549297270778805
+"144",0.00682798258030921,2,-0.383606471237968
+"145",0.0506687672308438,1,0.0628969594709541
+"146",-0.0326287236051719,2,0.307802130858709
+"147",0.0315667110616823,1,-0.0491288740872056
+"148",0.0234248510551544,2,-0.886174605827197
+"149",0.0481635795365275,1,-0.353063829906177
+"150",-0.0204159335953801,1,-0.373480626840549
+"151",-0.0144661128213790,2,1.00020535625734
+"152",-0.0238605666750649,2,-0.37293648383054
+"153",0.0669524872438994,1,0.970846742038665
+"154",0.0162224364339952,1,-0.288023336074307
+"155",0.0262431872112602,1,0.234872138823723
+"156",0.0863676918748504,1,-0.124107339307035
+"157",-0.0357602082230672,2,-0.860582860820529
+"158",0.0428400556861055,1,-0.297747269417959
+"159",0.0168487333575743,2,0.109903610414647
+"160",0.00714113104209875,2,-0.206224671104973
+"161",-0.0132135189742209,2,-0.327867194019532
+"162",0.131461070372543,1,-0.213564690106344
+"163",-0.0113346282034837,2,0.188385676330015
+"164",0.00557538873315109,1,-0.628807957951394
+"165",-0.0135266674360104,2,0.669583796395588
+"166",-0.043275771306016,2,-0.343884620646265
+"167",-0.0708328359434948,1,-0.190185480431738
+"168",0.00150445872988718,2,-0.320328578790684
+"169",0.063194705702425,1,0.323386845722763
+"170",-0.0160318551303266,2,-0.466837070291079
+"171",-0.0150924097449580,1,-0.443407572986743
+"172",-0.0598726397808612,2,-0.134811390846991
+"173",0.0159092879722056,1,0.482090992234558
+"174",-0.0664487574784414,1,-0.0170463331877988
+"175",-0.0946321190394993,1,-0.190324801658185
+"176",-0.0263657543693812,2,0.133819910273860
+"177",0.0259300387494707,1,0.635173662501035
+"178",0.0184144756665219,2,0.00228391995819166
+"179",0.0162224364339952,2,-0.258437031861175
+"180",0.0412743133771578,2,0.0283400108555913
+"181",0.00588853719494063,1,-0.645215565877466
+"182",0.0500424703072647,2,-0.291670337298211
+"183",0.0891860280309562,1,-0.327065894289160
+"184",-0.00162702588800815,1,0.242737144450905
+"185",-0.0260526059075917,2,0.57810653696704
+"186",-0.0248000120604336,1,-0.541941213451622
+"187",0.0575580333902134,1,-0.633212087112255
+"188",-0.082106180567918,2,0.500496715369151
+"189",0.0707102687853738,2,-0.052842886971195
+"190",0.00307020103883484,2,-0.244280532233061
+"191",-0.005071658967693,2,1.13589518632790
+"192",-0.0761563597939169,1,0.516233237416555
+"193",0.0212328118226277,1,-0.120931696200069
+"194",0.0838625041805342,1,-0.298112413451003
+"195",-0.0495387405418066,2,-0.460823957234195
+"196",0.048476727998317,1,-0.53750964944165
+"197",0.0362639379885253,2,-0.222956248715534
+"198",0.0134041002778894,1,-0.534628063085933
+"199",-0.03388131745233,2,-0.00536312114999693
+"200",-0.0157187066685371,2,-0.601310067820068
+"201",0.0491030249218961,2,0.51371538232261
+"202",-0.00788999512379879,1,-0.443235207931272
+"203",0.0910649188016934,1,-0.0545450835543364
+"204",0.0566185880048449,1,0.159594834986961
+"205",-0.00726369820021974,1,0.817680352105999
+"206",-0.0470335528474903,2,-0.920940961348847
+"207",0.038455977221052,1,0.206785551831567
+"208",-0.0138398158977999,2,0.0786089094577416
+"209",0.0378296802974729,2,-0.517512336320252
+"210",-0.0166581520539057,1,-0.69987268730616
+"211",0.0472241341511589,2,0.594013625246057
+"212",-0.0166581520539057,2,-0.832652369978527
+"213",0.0312535625998928,2,-0.646413025368303
+"214",-0.00100072896442909,2,-0.440536367839533
+"215",-0.0811667351825494,2,-0.279369474909596
+"216",-0.0320024266815928,1,-0.0452140231102436
+"217",0.0741549018650587,1,0.137324260072112
+"218",0.0368902349121043,2,0.699084005257896
+"219",0.014343545663258,2,0.809085151068957
+"220",-0.0742774690231797,2,0.605749454506367
+"221",-0.0332550205287509,1,-0.124684466736664
+"222",0.000878161806308105,2,-0.181486885774829
+"223",-0.0476598497710694,1,1.04353748120419
+"224",-0.0601857882426507,2,0.288952596833982
+"225",-0.0413968805352788,2,-0.104429039490037
+"226",-0.0435889197678055,1,0.0800869382183447
+"227",-0.0248000120604336,1,-0.144169895377154
+"228",-0.0157187066685371,1,-0.0464432100385457
+"229",0.00808057642746734,2,0.478240259012026
+"230",-0.000687580502639557,1,-0.467440941086978
+"231",0.155886650392127,1,0.239431491079654
+"232",0.00870687335104641,2,0.2562547807972
+"233",0.0572448849284239,1,0.86860230418135
+"234",-0.034507614375909,2,-0.423459070947301
+"235",-0.0241737151368545,2,0.310211050362970
+"236",-0.034507614375909,1,-0.295906130057979
+"237",0.0707102687853738,2,-0.86617486548278
+"238",-0.00100072896442909,2,-0.121778887044718
+"239",-0.00757684666200928,1,0.776213597614415
+"240",0.0387691256828415,2,0.509279639297807
+"241",-0.00225332281158722,1,0.465384478561689
+"242",0.0274957810584184,1,0.469496518921371
+"243",-0.0677013513255995,1,-0.308746203780249
+"244",-0.0160318551303266,1,-0.46235848664352
+"245",-0.0489124436182275,1,0.205409229630935
+"246",-0.058620045933703,2,0.261398866276518
+"247",0.0509819156926333,2,-0.440149176757358
+"248",-0.0185370428246429,2,-0.340825239203231
+"249",0.128016437292858,2,0.273551295992088
+"250",0.0293746718291555,2,-0.0150998906400583
+"251",-0.039204841302752,2,0.576834918553312
+"252",0.0487898764601065,1,-0.205915937224996
+"253",0.0528608064633705,2,-0.553196865177558
+"254",0.0566185880048449,2,-0.543721288333984
+"255",-0.0122740735888523,1,0.522487158063439
+"256",-0.0194764882100115,2,0.463745159249026
+"257",-0.0197896366718010,2,0.841549445924151
+"258",-0.0235474182132754,1,-0.453687910246368
+"259",0.0528608064633705,1,-0.458440156334343
+"260",0.0129343775852051,2,-0.467864695867239
+"261",-0.0313761297580137,2,-0.472283529481048
+"262",-0.0257394574458021,2,-0.186430934773366
+"263",0.0174750302811533,1,0.321642638528018
+"264",-0.0326287236051719,1,0.352069267692134
+"265",-0.00976888589453599,1,0.02668959086612
+"266",-0.00287961973516629,1,-0.556132391455717
+"267",-0.0366996536084358,1,-0.387257292601137
+"268",0.0794784257154807,2,-0.324131357308187
+"269",0.0375165318356834,1,0.0827698839729645
+"270",-0.0103951828181151,2,-0.093755609745107
+"271",-0.0473467013092799,1,0.191572236429703
+"272",-0.0210422305189592,1,-0.259424141806862
+"273",-0.0664487574784414,2,0.29937915243771
+"274",0.0328193049088404,1,0.376184708733085
+"275",-0.00319276819695581,2,-0.683575654018569
+"276",-0.0154055582067476,1,-0.64142305877968
+"277",0.0916912157252725,2,0.811986459824865
+"278",-0.078035250564654,2,-0.298077785935728
+"279",0.0196670695136800,1,-0.0758214988112154
+"280",-0.0263657543693812,1,0.827132228117798
+"281",0.0105857641217836,1,0.689895342645724
+"282",-0.0304366843726451,1,-0.184184898826604
+"283",0.102964560349696,2,0.847194957424707
+"284",-0.0363865051466462,2,0.806409840008277
+"285",-0.0451546620767532,1,0.0827048684085705
+"286",0.0212328118226277,2,0.552824579772346
+"287",-0.0864902590329714,2,-0.354242885013583
+"288",0.125198101136752,2,0.653520053265854
+"289",0.0563054395430553,1,-0.235849267757233
+"290",0.05317395492516,1,-1.15340165541335
+"291",0.0168487333575743,1,0.961697254069715
+"292",0.0428400556861055,2,0.461276319877892
+"293",-0.0686407967109681,2,-0.0341884331315262
+"294",0.0425269072243159,2,0.19050070101563
+"295",0.0177881787429428,1,-0.320894539927312
+"296",-0.0129003705124313,1,-0.687711338067914
+"297",-0.024486863598644,2,-0.0112816932009854
+"298",-0.024486863598644,2,-0.628420721133336
+"299",-0.0755300628703378,1,0.108339202697929
+"300",-0.0219816759043277,1,-0.299121148314735
+"301",-0.0135266674360104,2,0.504288281290109
+"302",0.0300009687527346,1,-0.49674221648836
+"303",0.0271826325966288,2,-0.0648277245363391
+"304",0.0202933664372591,2,0.0653229380005493
+"305",0.116429944206646,1,1.09697612700141
+"306",0.0162224364339952,1,-0.0578323225188244
+"307",-0.0248000120604336,1,-0.716688114767039
+"308",0.0356376410649462,1,0.0874474382931314
+"309",-0.0814798836443389,2,0.128350908869302
+"310",0.0700839718617947,1,-0.114604975474514
+"311",0.0149698425868371,2,-0.62242646270281
+"312",0.0606895180081088,2,0.103579664573858
+"313",-0.0141529643595894,2,0.266005125434976
+"314",0.0196670695136800,1,-0.413634930912108
+"315",-0.00100072896442909,2,0.0151321906456678
+"316",0.0206065148990486,2,-0.0673849072308246
+"317",-0.0213553789807487,1,0.0135990739864607
+"318",0.0741549018650587,2,0.324087630938248
+"319",0.00870687335104641,2,-0.427399230946266
+"320",-0.0545491159304391,2,0.042775486747467
+"321",0.092004364187062,2,-0.605344789864081
+"322",0.0365770864503148,2,-0.204436152405274
+"323",-0.0360733566848567,1,-0.226138837001874
+"324",-0.00444536204411395,1,0.170709352903985
+"325",0.077912683406533,2,0.537519459868399
+"326",0.0566185880048449,2,-0.147282475494555
+"327",0.00119131026809764,1,-0.323430494775891
+"328",0.0249905933641021,2,0.108292017818686
+"329",-0.0232342697514859,2,-0.826538205190531
+"330",-0.029184090525487,1,0.24584441334714
+"331",0.0368902349121043,1,0.573723086073314
+"332",-0.0464072559239113,1,0.79656132242823
+"333",-0.0113346282034837,2,0.00946238474567895
+"334",-0.00162702588800815,1,-0.124520035965299
+"335",-0.0576806005483345,1,-0.259878130786406
+"336",-0.00663740127664067,2,0.0555307997381935
+"337",0.0894991764927457,2,0.555424791964305
+"338",0.00714113104209875,1,-0.636112973637205
+"339",0.0240511479787335,2,0.873339312894887
+"340",0.0566185880048449,2,-0.394814482694516
+"341",-0.00381906512053488,2,0.739017674428192
+"342",0.00119131026809764,1,0.708961041328093
+"343",0.0181013272047324,1,0.00403126578142898
+"344",0.00870687335104641,2,-0.276137519375382
+"345",0.0644472995495832,2,0.502910779173363
+"346",0.057871181852003,1,-0.0156541427576098
+"347",0.127390140369279,1,-0.461785423626198
+"348",-0.0125872220506418,1,-0.169076596135421
+"349",-0.0294972389872765,2,0.350512955716197
+"350",-0.0470335528474903,1,-0.124228415607815
+"351",-0.0175975974392743,1,-0.131461613178762
+"352",-0.0695802420963367,1,-0.205628872696091
+"353",-0.0971373067338155,1,-0.0878584523532161
+"354",-0.00319276819695581,2,-0.495971604169367
+"355",0.0888728795691667,1,0.453324913491325
+"356",-0.0216685274425382,1,-0.458564307257987
+"357",0.0162224364339952,1,-0.556629174086865
+"358",-0.0301235359108556,1,0.169271197644518
+"359",-0.0341944659141195,2,0.0657618936180249
+"360",0.0174750302811533,1,1.25141355432077
+"361",-0.0132135189742209,2,0.652499667425962
+"362",-0.0482861466946485,2,0.704038829561223
+"363",-0.0266789028311707,1,0.669786704168092
+"364",-0.0282446451401184,1,-0.825099908269144
+"365",0.00494909180957202,1,0.878493590561456
+"366",0.00526224027136155,2,0.460202718189125
+"367",0.0318798595234718,1,-0.281858889818106
+"368",0.033758750294209,1,-0.235429645519174
+"369",-0.0100820343563255,1,-0.749168455422644
+"370",-0.00381906512053488,2,0.0138580627952098
+"371",-0.0125872220506418,2,-0.222636705057443
+"372",-0.0191633397482220,1,-0.102899440319366
+"373",0.0127778033543103,1,-0.364792071375576
+"374",-0.0570543036247554,2,0.418437419922108
+"375",-0.0705196874817053,2,0.148241329965757
+"376",0.0224854056697859,1,0.430891807354808
+"377",0.130208476525385,2,-0.741549127948163
+"378",0.0447189464568426,1,0.684173593258704
+"379",0.0108989125835731,1,0.72101144786046
+"380",-0.115613065979398,2,-0.657949812502163
+"381",-0.0442152166913845,2,-0.896421924067635
+"382",-0.0257394574458021,1,0.0962925069688172
+"383",-0.072711726714232,2,-1.00276025631586
+"384",-0.0288709420636975,1,-0.157806820134940
+"385",0.0869939887984295,1,-0.445362055938887
+"386",-0.0611252336280193,1,0.84021857926248
+"387",-0.0175975974392743,2,-0.251533189535103
+"388",-0.0172844489774848,2,0.758893789787943
+"389",-0.005071658967693,1,-0.395976152709988
+"390",-0.0166581520539057,1,-0.362704477405226
+"391",-0.0232342697514859,1,0.240165673609364
+"392",-0.0504781859271752,2,-0.155741439704364
+"393",0.0365770864503148,1,0.0385290544410537
+"394",-0.0232342697514859,2,-0.238860553149526
+"395",-0.0545491159304391,2,0.293301706277455
+"396",-0.0216685274425382,2,0.831706790819527
+"397",-0.0542359674686496,1,-0.440514782297251
+"398",-0.0583068974719135,2,0.218870588212521
+"399",0.0321930079852613,2,0.500744829653927
+"400",0.0118383579689417,1,0.262479865365506
+"401",-0.0354470597612776,2,0.0459955002977468
+"402",-0.05392281900686,2,-0.0247330661767469
+"403",0.0202933664372591,1,0.170742902946737
+"404",-0.0238605666750649,2,0.199286515264368
+"405",-0.0279314966783289,2,1.08912576788426
+"406",-0.10089508827529,1,0.114498290097875
+"407",-0.0370128020702253,2,-0.0846106975545163
+"408",0.0397085710682101,2,-0.341931668571862
+"409",0.0193539210518905,2,0.161218178259627
+"410",0.0729023080179005,1,0.0829112288198928
+"411",0.0372033833738938,1,0.480091172076597
+"412",-0.0723985782524425,2,-0.182281092461526
+"413",0.0130909518160999,2,0.301199977328185
+"414",0.00714113104209875,2,0.0875330300958936
+"415",0.117056241130225,1,-0.464798937851476
+"416",0.0472241341511589,2,0.0928613558403242
+"417",0.0181013272047324,2,0.518938399652306
+"418",-0.00131387742621863,2,-0.915794067370554
+"419",0.0941964034195887,2,-0.0849758660905434
+"420",-0.0573674520865449,2,-0.557819575895558
+"421",0.0346981956795776,2,0.146580008210001
+"422",0.0450320949186321,1,0.180578242378216
+"423",0.0644472995495832,1,0.207776620969095
+"424",0.0735286049414796,1,-0.392666088043916
+"425",-0.00381906512053488,1,-0.627260070295178
+"426",-0.112794729823292,2,0.260190647274243
+"427",0.0688313780146366,1,-0.386184997207579
+"428",-0.062690975936967,1,-0.503984283937765
+"429",0.0215459602844172,1,0.297983166681027
+"430",0.0415874618389473,2,-0.126484961821684
+"431",0.0453452433804217,2,0.576267745573508
+"432",-0.0470335528474903,1,-0.461945840462522
+"433",0.0447189464568426,2,-0.484434347988346
+"434",0.0199802179754696,2,-0.180198683463334
+"435",0.0108989125835731,2,-0.556213330349359
+"436",0.0046359433477825,2,-0.47603482348101
+"437",-0.0470335528474903,2,-0.290496276509039
+"438",-0.00256647127337676,1,-0.174951863141946
+"439",0.0791652772536912,1,-0.0941605505892384
+"440",-0.0138398158977999,1,0.0900586677437571
+"441",0.0152829910486266,2,0.283684348322489
+"442",0.0278089295202079,2,-0.215872199044323

package/dist/vfs/usr/lib/R/library/stats/tests/simulate.R

@@ -0,0 +1,87 @@
+## tests of the simulate.lm method, added Feb 2009
+
+options(digits = 5)
+
+## cases should be named
+hills <- readRDS("hills.rds") # copied from package MASS
+fit1 <- lm(time ~ dist, data = hills)
+set.seed(1)
+simulate(fit1, nsim = 3)
+
+## and weights should be taken into account
+fit2 <- lm(time ~ -1 + dist + climb, hills[-18, ], weight = 1/dist^2)
+coef(summary(fit2))
+set.seed(1); ( ys <- simulate(fit2, nsim = 3) )
+for(i in seq_len(3))
+    print(coef(summary(update(fit2, ys[, i] ~ .))))
+## should be identical to glm(*, gaussian):
+fit2. <- glm(time ~ -1 + dist + climb, family=gaussian, data=hills[-18, ],
+             weight = 1/dist^2)
+set.seed(1); ys. <- simulate(fit2., nsim = 3)
+stopifnot(all.equal(ys, ys.))
+
+## Poisson fit
+load("anorexia.rda") # copied from package MASS
+fit3 <- glm(Postwt ~ Prewt + Treat + offset(Prewt),
+            family = gaussian, data = anorexia)
+coef(summary(fit3))
+set.seed(1)
+simulate(fit3, nsim = 8)
+
+## two-column binomial fit
+ldose <- rep(0:5, 2)
+numdead <- c(1, 4, 9, 13, 18, 20, 0, 2, 6, 10, 12, 16)
+sex <- factor(rep(c("M", "F"), c(6, 6)))
+SF <- cbind(numdead, numalive = 20 - numdead)
+fit4 <- glm(SF ~ sex + ldose - 1, family = binomial)
+coef(summary(fit4))
+set.seed(1)
+( ys <- simulate(fit4, nsim = 3) )
+for(i in seq_len(3))
+    print(coef(summary(update(fit4, ys[, i] ~ .))))
+
+## same via proportions
+fit5 <- glm(numdead/20 ~ sex + ldose - 1, family = binomial,
+            weights = rep(20, 12))
+set.seed(1)
+( ys <- simulate(fit5, nsim = 3) )
+for(i in seq_len(3))
+    print(coef(summary(update(fit5, ys[, i] ~ .))))
+
+
+## factor binomial fit
+load("birthwt.rda") # copied from package MASS
+bwt <- with(birthwt, {
+    race <- factor(race, labels = c("white", "black", "other"))
+    table(ptl)
+    ptd <- factor(ptl > 0)
+    table(ftv)
+    ftv <- factor(ftv)
+    levels(ftv)[-(1:2)] <- "2+"
+    data.frame(low = factor(low), age, lwt, race,
+               smoke = (smoke > 0), ptd, ht = (ht > 0), ui = (ui > 0), ftv)
+})
+fit6 <- glm(low ~ ., family = binomial, data = bwt)
+coef(summary(fit6))
+set.seed(1)
+ys <- simulate(fit6, nsim = 3)
+ys[1:10, ]
+for(i in seq_len(3))
+    print(coef(summary(update(fit6, ys[, i] ~ .))))
+
+## This requires MASS::gamma.shape
+if(!require("MASS", quietly = TRUE)) {
+    message("skipping tests requiring the MASS package")
+    q()
+}
+
+## gamma fit, from example(glm)
+clotting <- data.frame(u = c(5,10,15,20,30,40,60,80,100),
+                       lot1 = c(118,58,42,35,27,25,21,19,18))
+fit7 <- glm(lot1 ~ log(u), data = clotting, family = Gamma)
+coef(summary(fit7))
+set.seed(1)
+( ys <- simulate(fit7, nsim = 3) )
+for(i in seq_len(3))
+    print(coef(summary(update(fit7, ys[, i] ~ .))))
+