Oh, interesting - here I thought I was getting a confidence region for the model (which of course you're right has two parameters) and in fact confint is giving me the confidence interval for each of the two parameters in the model.
The ellipse package does a nice job of helping me visualize that. Thanks for clearing that up. On Wed, Mar 28, 2012 at 1:48 PM, peter dalgaard <pda...@gmail.com> wrote: > > On Mar 28, 2012, at 21:33 , Benjamin Caldwell wrote: > > > Hello all, > > > > I'm trying to use confint from the MASS package to compute confidence > > intervals for an nls object. When I plot the results, however, they don't > > make sense - lines cross over the fitted model or just don't match the > > data. Code is : > > > > Thanks for help > > > > dat<-data.frame(a,b) > > with(dat, plot(a,b)) > > model<-(nls(b~(1/exp(a*x))*n, data=dat, start=list(x=.001,n=20), > > na.action="na.omit")) > > with(dat, plot(a,b)) > > x1<-summary(model)$coefficients[1,1] > > n1<-summary(model)$coefficients[2,1] > > lines((1/exp(c(0:30)*x1)*n1)) > > int<-MASS:::confint.nls(model) > > lines((1/exp(c(0:30)*int[1,1])*int[2,1]),lty=2) > > lines((1/exp(c(0:30)*int[2,1])*int[2,2]),lty=2) > > > > Looks like you just haven't understood how CI's work. There's no reason to > believe that you can combine the extremes of confidence intervals for two > parameters and get an interval for a fitted value. For one thing, it is > quite common that a simultaneous confidence region for two parameters is > like a narrow ellipse due to correlation of the estimates. > > This is a matter of statistical theory, not of R. > > The last lines() look just unintended, btw. Shouldn't int[2,1] be [1,2]?? > > > > > "","a" > > "1",NA > > "2",5.8 > > "3",5.15 > > "4",NA > > "5",5.7 > > "6",12.35 > > "7",10.9 > > "8",10.65 > > "9",18.7 > > "10",5.35 > > "11",12 > > "12",NA > > "13",14.8 > > "14",13.3 > > "15",15.6 > > "16",19.8 > > "17",NA > > "18",NA > > "19",NA > > "20",NA > > "21",NA > > "22",NA > > "23",NA > > "24",NA > > "25",NA > > "26",NA > > "27",NA > > "28",NA > > "29",7.1 > > "30",NA > > "31",NA > > "32",15.15 > > "33",NA > > "34",11.6 > > "35",NA > > "36",NA > > "37",6.35 > > "38",18.45 > > "39",16.65 > > "40",NA > > "41",9.8 > > "42",7.35 > > "43",7.35 > > "44",11.55 > > "45",18.1 > > "46",5.65 > > "47",4.25 > > "48",NA > > "49",6.45 > > "50",5.2 > > "51",5.45 > > "52",NA > > "53",NA > > "54",9.8 > > "55",6.35 > > "56",21.95 > > "57",NA > > "58",NA > > "59",11.4 > > "60",NA > > "61",NA > > "62",10.65 > > "63",NA > > "64",NA > > "65",4.8 > > "66",7.35 > > "67",17.55 > > "68",5.55 > > "69",8.8 > > "70",8.3 > > "71",10.8 > > "72",11.1 > > "73",5.3 > > "74",NA > > "75",NA > > "76",7.55 > > "77",8.5 > > "78",NA > > "79",21.55 > > "80",NA > > "81",7 > > "82",5.4 > > "83",NA > > "84",NA > > "85",7.45 > > "86",5.5 > > "87",8.05 > > "88",16.35 > > "89",5.25 > > "90",6.85 > > "91",4.7 > > "92",3.25 > > "93",5.45 > > "94",8.15 > > "95",2.9 > > "96",3.05 > > "97",7.9 > > "98",6.2 > > "99",5.85 > > "100",6.7 > > "101",17.45 > > "102",4.3 > > "103",9.85 > > "104",12.6 > > "105",12.75 > > "106",3.95 > > "107",NA > > "108",14.4 > > "109",7.4 > > "110",NA > > "111",4.95 > > "112",4.75 > > "113",4.2 > > "114",5.5 > > "115",6.2 > > "116",9.6 > > "117",NA > > "118",12.95 > > "119",9.1 > > "120",25.9 > > "121",7.55 > > "122",12.3 > > "123",11.2 > > "124",8.35 > > "125",NA > > "126",6.95 > > "127",20.9 > > "128",NA > > "129",NA > > "130",6.75 > > "131",6.55 > > "132",NA > > "133",10.25 > > "134",8.3 > > "135",NA > > "136",10.35 > > "137",4.8 > > "138",12.25 > > "139",9.45 > > "140",7.55 > > "141",5.15 > > "142",9 > > "143",4.95 > > "144",NA > > "145",8.4 > > "146",6.65 > > "147",11.15 > > "148",7.65 > > "149",NA > > "150",NA > > "151",NA > > "152",NA > > "153",12.95 > > "154",NA > > "155",4.6 > > "156",4.8 > > "157",10.95 > > "158",4.25 > > "159",4.1 > > "160",5.3 > > "161",3.8 > > "162",12.75 > > "163",NA > > "164",10.8 > > "165",NA > > "166",8.65 > > "167",25.45 > > "168",NA > > "169",7.65 > > "170",18.4 > > "171",9.1 > > "172",5.7 > > "173",6.15 > > "174",NA > > "175",NA > > "176",4.5 > > "177",8.45 > > "178",NA > > "179",NA > > "180",NA > > "181",8.55 > > "182",9.15 > > "183",12.9 > > "184",27.65 > > "185",NA > > "186",8.3 > > "187",12.8 > > "188",NA > > "189",5.85 > > "190",NA > > "191",7 > > "192",11.65 > > "193",8.15 > > "194",24.45 > > "195",15.25 > > "196",10.5 > > "197",NA > > "198",3.6 > > "199",NA > > "200",5.55 > > "201",NA > > "202",10.3 > > "203",NA > > "204",4.6 > > "205",5.95 > > "206",10.15 > > "207",5.7 > > "208",23.2 > > "209",11.95 > > "210",NA > > "211",6.05 > > "212",5.55 > > "213",NA > > "214",NA > > "215",NA > > "216",NA > > "217",16.4 > > "218",4.65 > > "219",16.35 > > "220",7.95 > > "221",7.45 > > "222",NA > > "223",7.9 > > "224",21.15 > > "225",NA > > "226",NA > > "227",NA > > "228",11.15 > > "229",9.15 > > "230",11.35 > > "231",4.75 > > "232",3.85 > > "233",NA > > "234",5.05 > > "235",NA > > "236",12.7 > > "237",6.35 > > "238",NA > > "239",NA > > "240",NA > > "241",10.15 > > "242",5.15 > > "243",NA > > "244",NA > > "245",6.4 > > "246",7.15 > > "247",NA > > "248",16.5 > > "249",NA > > "250",NA > > "251",NA > > "252",7.15 > > "253",6.7 > > "254",NA > > "255",NA > > "256",NA > > "257",NA > > "258",NA > > "259",NA > > "260",NA > > "261",4.1 > > "262",4.55 > > "263",4.45 > > "264",NA > > "265",7.2 > > "266",6.1 > > "267",6 > > "268",NA > > "269",8.75 > > "270",NA > > "271",5.6 > > "272",NA > > "273",NA > > "274",NA > > "275",NA > > "276",NA > > "277",NA > > "278",NA > > "279",NA > > "280",NA > > "281",NA > > "282",NA > > "283",NA > > "284",NA > > "285",NA > > "286",NA > > "287",NA > > "288",8.1 > > "289",NA > > "290",NA > > "291",NA > > "292",NA > > "293",NA > > "294",NA > > "295",NA > > "296",NA > > "297",8.15 > > "298",7.7 > > "299",NA > > "300",NA > > "301",26.75 > > "302",21 > > "303",10.45 > > "304",NA > > "305",6.7 > > "306",20.5 > > "307",NA > > "308",10.5 > > "309",NA > > "310",NA > > "311",NA > > "312",NA > > "313",NA > > "314",5.65 > > "315",12.75 > > "316",5 > > "317",5.85 > > "318",3.55 > > "319",4.05 > > "320",6.4 > > "321",4.75 > > "322",NA > > "323",NA > > "324",NA > > "325",2.75 > > "326",NA > > "327",4.9 > > "328",5.05 > > "329",5.3 > > "330",NA > > "331",NA > > "332",NA > > "333",NA > > "334",NA > > "335",6.95 > > "336",6.4 > > "337",6.1 > > "338",NA > > "339",11.75 > > "340",3.35 > > "341",7.45 > > "342",6.9 > > "343",5.75 > > "344",6.1 > > "345",NA > > "346",NA > > "347",5 > > "348",5.85 > > "349",NA > > "350",5.5 > > "351",6.65 > > "352",11.1 > > "353",10.95 > > "354",16.6 > > "355",7.2 > > "356",6.5 > > "357",NA > > "358",8.45 > > "359",NA > > "360",8.3 > > "361",17.05 > > "362",NA > > "363",NA > > "364",NA > > "365",NA > > "366",12.7 > > "367",NA > > "368",8.05 > > "369",9.7 > > "370",NA > > "371",12.35 > > "372",4.85 > > "373",5.5 > > "374",NA > > "375",4.9 > > "376",NA > > "377",NA > > "378",15.05 > > "379",NA > > "380",NA > > "381",8.4 > > "382",NA > > "383",NA > > "384",5.15 > > "385",11.4 > > "386",NA > > "387",8 > > "388",7.45 > > "389",8.7 > > "390",9.05 > > "391",15.1 > > "392",NA > > "393",NA > > "394",NA > > "395",NA > > "396",7.4 > > "397",10.6 > > "398",20.2 > > "399",10.95 > > "400",7.6 > > "401",NA > > "402",NA > > "403",NA > > "404",8.3 > > "405",9.65 > > "406",14.75 > > "407",NA > > "408",2.9 > > "409",NA > > "410",NA > > "411",NA > > "412",NA > > "413",NA > > "414",NA > > "415",NA > > "416",2.55 > > "417",3.2 > > "418",4.05 > > "419",9.05 > > "420",3.25 > > "421",6.7 > > "422",NA > > "423",NA > > "424",NA > > "425",7.25 > > "426",NA > > "427",NA > > "428",NA > > "429",8.8 > > "430",5.05 > > "431",3.6 > > "432",7.7 > > "433",14.45 > > "434",10.2 > > "435",NA > > "436",NA > > "437",12.95 > > "438",8.8 > > "439",4.5 > > "440",5.3 > > "441",17.7 > > "442",10.2 > > "443",5.55 > > "444",3.9 > > "445",20 > > "446",12.2 > > "447",10.8 > > "448",NA > > "449",NA > > "450",NA > > "451",NA > > "452",NA > > "453",NA > > "454",NA > > "455",NA > > "456",NA > > "457",NA > > "458",NA > > "459",NA > > "460",NA > > "461",NA > > "462",NA > > "463",NA > > "464",NA > > > > > > "","b" > > "1",NA > > "2",243.085758119756 > > "3",274.339641306582 > > "4",NA > > "5",418.039560741661 > > "6",46.5033624229099 > > "7",79.9087810465099 > > "8",215.216454070312 > > "9",107.035742459874 > > "10",278.567219708664 > > "11",283.033857603722 > > "12",NA > > "13",98.2911978484231 > > "14",173.670430606987 > > "15",174.110803357204 > > "16",95.6489613471215 > > "17",NA > > "18",NA > > "19",NA > > "20",NA > > "21",NA > > "22",NA > > "23",NA > > "24",NA > > "25",NA > > "26",NA > > "27",NA > > "28",NA > > "29",222.264934489499 > > "30",NA > > "31",NA > > "32",181.181931517831 > > "33",NA > > "34",189.486103379064 > > "35",NA > > "36",NA > > "37",389.654391470535 > > "38",41.7095904848339 > > "39",199.224632198148 > > "40",NA > > "41",144.781978192755 > > "42",118.095389529608 > > "43",97.787914705318 > > "44",83.4191809696678 > > "45",22.9497113255919 > > "46",164.196125438034 > > "47",201.514570499276 > > "48",NA > > "49",273.786029849166 > > "50",350.184410972518 > > "51",271.772897276746 > > "52",NA > > "53",NA > > "54",57.3742783139797 > > "55",135.005703137939 > > "56",73.4793388933424 > > "57",NA > > "58",NA > > "59",90.5909657589153 > > "60",NA > > "61",NA > > "62",204.685254300838 > > "63",NA > > "64",NA > > "65",296.182129717343 > > "66",237.901941745774 > > "67",26.2713800700854 > > "68",290.94798502905 > > "69",196.657888168312 > > "70",117.403375207839 > > "71",62.6210050808502 > > "72",238.367478653146 > > "73",423.550511158662 > > "74",NA > > "75",NA > > "76",86.4011335925654 > > "77",189.901311972126 > > "78",NA > > "79",42.2757840208271 > > "80",NA > > "81",269.961077961568 > > "82",330.355055134178 > > "83",NA > > "84",NA > > "85",109.489247782511 > > "86",398.85189091078 > > "87",83.9098820341953 > > "88",19.099595280838 > > "89",335.299812015185 > > "90",100.895688113992 > > "91",1118.39580060812 > > "92",849.554527639962 > > "93",719.97170036898 > > "94",194.22954700283 > > "95",769.06697097888 > > "96",616.307954967909 > > "97",87.5712669002847 > > "98",209.491608317492 > > "99",346.485279870696 > > "100",209.038653488697 > > "101",38.4885783689614 > > "102",482.396892666224 > > "103",46.6543473658414 > > "104",86.0614174709695 > > "105",94.6675592180665 > > "106",364.691547572522 > > "107",NA > > "108",22.1444582966237 > > "109",65.2632415821519 > > "110",NA > > "111",256.649238826438 > > "112",358.488582833752 > > "113",167.480047946795 > > "114",133.395197080003 > > "115",206.497073616016 > > "116",309.82110289549 > > "117",NA > > "118",58.8841277432949 > > "119",135.420911731001 > > "120",210.850472803875 > > "121",221.130031001797 > > "122",124.71356286144 > > "123",101.575120357184 > > "124",122.952071860572 > > "125",NA > > "126",168.29788305434 > > "127",58.3305162858794 > > "128",NA > > "129",NA > > "130",181.559393875159 > > "131",331.311293106077 > > "132",NA > > "133",109.86671013984 > > "134",121.039595916773 > > "135",NA > > "136",85.2561644420014 > > "137",312.664652654034 > > "138",65.5274652322821 > > "139",101.91483647878 > > "140",167.593286653993 > > "141",280.265800316644 > > "142",216.462079849497 > > "143",548.087924920015 > > "144",NA > > "145",131.998586357886 > > "146",286.619749998346 > > "147",102.141313893177 > > "148",117.264972343485 > > "149",NA > > "150",NA > > "151",NA > > "152",NA > > "153",113.125468491445 > > "154",NA > > "155",352.411438880758 > > "156",211.378920104136 > > "157",79.3174233533614 > > "158",305.392211236165 > > "159",379.777459787097 > > "160",306.763657801127 > > "161",138.264461489544 > > "162",57.6510840426875 > > "163",NA > > "164",114.05654230619 > > "165",NA > > "166",73.3535181075661 > > "167",30.1969885863051 > > "168",NA > > "169",74.727481088243 > > "170",27.4490626249513 > > "171",60.5147651269554 > > "172",124.529864514207 > > "173",324.04388451964 > > "174",NA > > "175",NA > > "176",76.7305479978012 > > "177",141.76479574984 > > "178",NA > > "179",NA > > "180",NA > > "181",249.359182498561 > > "182",476.357494948963 > > "183",227.926869849431 > > "184",17.5796801886606 > > "185",NA > > "186",170.49723038971 > > "187",282.643813167816 > > "188",NA > > "189",641.691040290414 > > "190",NA > > "191",63.4136760312407 > > "192",275.109664515532 > > "193",75.618292251539 > > "194",14.305823342762 > > "195",38.7276378619363 > > "196",25.9694101842224 > > "197",NA > > "198",478.408373757116 > > "199",NA > > "200",869.069331513861 > > "201",NA > > "202",182.314318589817 > > "203",NA > > "204",892.29584856816 > > "205",305.744509436339 > > "206",672.335950874083 > > "207",445.707551533863 > > "208",12.5317502633166 > > "209",38.4759962903837 > > "210",NA > > "211",212.57421756901 > > "212",331.56293467763 > > "213",NA > > "214",NA > > "215",NA > > "216",NA > > "217",34.9152680529153 > > "218",328.417415033223 > > "219",34.1980895739905 > > "220",119.856880530476 > > "221",396.637445081118 > > "222",NA > > "223",252.358750031467 > > "224",9.66303634761762 > > "225",NA > > "226",NA > > "227",NA > > "228",168.297883054341 > > "229",48.8184648811932 > > "230",78.6128269530143 > > "231",86.3382231996773 > > "232",1503.6967928908 > > "233",NA > > "234",723.909890963777 > > "235",NA > > "236",15.6017774362576 > > "237",166.007944753212 > > "238",NA > > "239",NA > > "240",NA > > "241",150.632644731352 > > "242",733.182882875488 > > "243",NA > > "244",NA > > "245",330.719935412929 > > "246",417.133651084072 > > "247",NA > > "248",61.7150954232608 > > "249",NA > > "250",NA > > "251",NA > > "252",141.800025569858 > > "253",183.195064090251 > > "254",NA > > "255",NA > > "256",NA > > "257",NA > > "258",NA > > "259",NA > > "260",NA > > "261",864.388798282983 > > "262",285.05957225472 > > "263",246.118039056964 > > "264",NA > > "265",52.3414468829288 > > "266",182.767273418611 > > "267",432.571861498821 > > "268",NA > > "269",169.883224955121 > > "270",NA > > "271",69.8934464987186 > > "272",NA > > "273",NA > > "274",NA > > "275",NA > > "276",NA > > "277",NA > > "278",NA > > "279",NA > > "280",NA > > "281",NA > > "282",NA > > "283",NA > > "284",NA > > "285",NA > > "286",NA > > "287",NA > > "288",246.357098549939 > > "289",NA > > "290",NA > > "291",NA > > "292",NA > > "293",NA > > "294",NA > > "295",NA > > "296",NA > > "297",162.258485337079 > > "298",111.980499340881 > > "299",NA > > "300",NA > > "301",413.635833239492 > > "302",309.745610424024 > > "303",337.97979475222 > > "304",NA > > "305",567.489490086716 > > "306",105.94110162362 > > "307",NA > > "308",801.46582331627 > > "309",NA > > "310",NA > > "311",NA > > "312",NA > > "313",NA > > "314",91.949830245299 > > "315",168.021077325632 > > "316",671.958488516754 > > "317",119.227776601595 > > "318",1396.20809560213 > > "319",671.279056273563 > > "320",44.8425280506631 > > "321",443.669254804288 > > "322",NA > > "323",NA > > "324",NA > > "325",504.138724448364 > > "326",NA > > "327",183.597690604735 > > "328",536.487248471443 > > "329",481.30225182997 > > "330",NA > > "331",NA > > "332",NA > > "333",NA > > "334",NA > > "335",91.2200696877966 > > "336",130.224513278441 > > "337",66.1062408468529 > > "338",NA > > "339",23.2516812114549 > > "340",187.774940692507 > > "341",119.215194523017 > > "342",246.105456978387 > > "343",352.235289780671 > > "344",139.77431091886 > > "345",NA > > "346",NA > > "347",377.877565921875 > > "348",203.011837850014 > > "349",NA > > "350",128.941141263523 > > "351",347.756069807037 > > "352",164.825229366915 > > "353",178.791336588081 > > "354",123.807653203851 > > "355",552.302921243519 > > "356",542.539228267281 > > "357",NA > > "358",239.059492974915 > > "359",NA > > "360",127.267724812698 > > "361",245.841233328256 > > "362",NA > > "363",NA > > "364",NA > > "365",NA > > "366",188.680850350096 > > "367",NA > > "368",271.772897276746 > > "369",44.6915431077315 > > "370",NA > > "371",263.443561258357 > > "372",493.418793500225 > > "373",765.493660662834 > > "374",NA > > "375",357.960135533491 > > "376",NA > > "377",NA > > "378",28.0957814638413 > > "379",NA > > "380",NA > > "381",214.436365198499 > > "382",NA > > "383",NA > > "384",361.898326128289 > > "385",68.8868802125085 > > "386",NA > > "387",273.282746706061 > > "388",246.860381693044 > > "389",468.619516623722 > > "390",237.008614166762 > > "391",75.8699338230915 > > "392",NA > > "393",NA > > "394",NA > > "395",NA > > "396",268.350571903631 > > "397",53.9016246265545 > > "398",243.048011884023 > > "399",94.6801412966441 > > "400",485.882128432227 > > "401",NA > > "402",NA > > "403",NA > > "404",651.638431613887 > > "405",521.099366371005 > > "406",149.651242602297 > > "407",NA > > "408",524.924318258604 > > "409",NA > > "410",NA > > "411",NA > > "412",NA > > "413",NA > > "414",NA > > "415",NA > > "416",549.534863956443 > > "417",269.394884425574 > > "418",373.889047012767 > > "419",93.6861570890115 > > "420",257.11477573381 > > "421",167.492630025372 > > "422",NA > > "423",NA > > "424",NA > > "425",301.34078193417 > > "426",NA > > "427",NA > > "428",NA > > "429",143.850904378011 > > "430",239.285970389312 > > "431",380.104593830115 > > "432",181.181931517831 > > "433",31.4426143654902 > > "434",52.6685809259471 > > "435",NA > > "436",NA > > "437",17.6652383229885 > > "438",97.1588107764366 > > "439",305.744509436339 > > "440",332.166874449356 > > "441",34.8775218171824 > > "442",65.8294351181451 > > "443",153.249717075498 > > "444",263.279994236848 > > "445",15.287225471817 > > "446",44.880274286396 > > "447",71.6675195781641 > > "448",NA > > "449",NA > > "450",NA > > "451",NA > > "452",NA > > "453",NA > > "454",NA > > "455",NA > > "456",NA > > "457",NA > > "458",NA > > "459",NA > > "460",NA > > "461",NA > > "462",NA > > "463",NA > > "464",NA > > > > [[alternative HTML version deleted]] > > > > ______________________________________________ > > R-help@r-project.org mailing list > > https://stat.ethz.ch/mailman/listinfo/r-help > > PLEASE do read the posting guide > http://www.R-project.org/posting-guide.html > > and provide commented, minimal, self-contained, reproducible code. > > -- > Peter Dalgaard, Professor, > Center for Statistics, Copenhagen Business School > Solbjerg Plads 3, 2000 Frederiksberg, Denmark > Phone: (+45)38153501 > Email: pd....@cbs.dk Priv: pda...@gmail.com > > > > > > > > > [[alternative HTML version deleted]] ______________________________________________ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
