[R] lme, nlsList, nlsList.selfStart
Prof Brian Ripley
ripley at stats.ox.ac.uk
Fri Feb 17 11:43:26 CET 2006
We don't have Dose, and I think that is where the error lies. If Dose
were part of mydata2, this is likely to work, but otherwise it is Dose
which has the wrong length.
?nlsList says
data: a data frame in which to interpret the variables named in
'model'.
and it means it: you must get all the variables from there.
On Fri, 17 Feb 2006, Patrick Giraudoux wrote:
> Spencer,
>
> Thanks for the hint. I did not dare to bore people with the full data
> set and though that this kind of error may have been trivial and often
> encountered (so leading to a short answer), even though I did not see
> related messages on the r-help list. I already did the checks suggested
> before posting, and was aware of the possible confusion between 1 and l
> (actually the variable names were not given by myself).
>
> It seems that the trouble comes when the grouping variable "Organ" is
> used. The best (?) I can do is to dump the data.frame here below.
>
> With this example, one can get exactly the same errors:
>
> mymod2<-nls(Conc~Dose * exp(lKe+lKa-lCl) *
> (exp(-exp(lKe)*Tps)-exp(-exp(lKa)*Tps)) /(exp(lKa)-exp(lKe)),
> data=mydata2,
> start= c(lKe=-2.77, lKa=-1.41, lCl=-1.13)
> )
>
> ... works well!!!
>
> but we get then:
>
> mymod3<-nlsList(Conc~Dose * exp(lKe+lKa-lCl) *
> (exp(-exp(lKe)*Tps)-exp(-exp(lKa)*Tps)) /(exp(lKa)-exp(lKe)) | Organ,
> data=mydata2,
> start= c(lKe=-2.77, lKa=-1.41, lCl=-1.13)
> )
> Error in model.frame(formula, rownames, variables, varnames, extras,
> extranames, :
> variable lengths differ
> Error in model.frame(formula, rownames, variables, varnames, extras,
> extranames, :
> variable lengths differ
> Error in model.frame(formula, rownames, variables, varnames, extras,
> extranames, :
> variable lengths differ
>
>
> > mymod4<-nlsList(SSfol,data=mydata2)
> Error in eval(expr, envir, enclos) : object "input" not found
> Error in eval(expr, envir, enclos) : object "input" not found
> Error in eval(expr, envir, enclos) : object "input" not found
>
>
> Sorry and apologise for the inconvenience met,
>
> Kind regards,
>
> Patrick
>
>
>
> # data.frame just to copy and past into R
>
> "mydata2" <-
> structure(list(Tps = c(1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 2, 3,
> 3, 3, 3, 3, 3, 4, 4, 4, 4, 4, 4, 5, 5, 5, 5, 5, 5, 6, 6, 6, 6,
> 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 8, 8, 8, 8, 8, 9, 9, 9,
> 9, 9, 9, 10, 10, 10, 10, 10, 10, 11, 11, 11, 11, 11, 11, 14,
> 14, 14, 14, 14, 17, 17, 17, 17, 17, 20, 20, 20, 20, 25, 28, 29,
> 50, 50, 50, 136, 136, 136, 136, 136, 136, 136, 136, 136, 136,
> 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 2, 3, 3, 3, 3, 3, 3, 4, 4, 4,
> 4, 4, 4, 5, 5, 5, 5, 5, 5, 6, 6, 6, 6, 6, 6, 7, 7, 7, 7, 7, 7,
> 7, 7, 7, 7, 8, 8, 8, 8, 8, 8, 9, 9, 9, 9, 9, 9, 10, 10, 10, 10,
> 10, 10, 11, 11, 11, 11, 11, 11, 14, 14, 14, 14, 14, 17, 17, 17,
> 17, 17, 20, 20, 20, 20, 25, 28, 29, 50, 50, 50, 136, 136, 136,
> 136, 136, 136, 136, 136, 136, 136, 1, 1, 1, 1, 1, 1, 2, 2, 2,
> 2, 2, 2, 3, 3, 3, 3, 3, 3, 4, 4, 4, 4, 4, 4, 5, 5, 5, 5, 5, 5,
> 6, 6, 6, 6, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 8, 8, 8, 8,
> 8, 9, 9, 9, 9, 9, 9, 10, 10, 10, 10, 10, 10, 11, 11, 11, 11,
> 11, 11, 14, 14, 14, 14, 14, 17, 17, 17, 17, 17, 20, 20, 20, 20,
> 25, 28, 29, 50, 50, 50, 136, 136, 136, 136, 136, 136, 136, 136,
> 136, 136), Conc = c(0, 0, 0, 0, 0, 0, 0, 0.807852503274902,
> 0.204371494701886,
> 0.579222129993907, 0.989062273721619, 0, 1.11728297897571,
> 1.41057428121324,
> 0.888883702851307, 1.259907624008, 1.45753269675829, 1.07077516747401,
> 0.843279379, 0, 0.763110069196737, 1.11297791434297, 1.10087763997637,
> 0.946929594501016, 1.33112168, 0.654041755, 0.694167499, 1.289548703,
> 1.117139864, 0.807196192, 0.720221376552025, 0.560082823, 0.476583438,
> 2.590855204, 0.51510972, 1.072946887, 0.537999938614396, 0.886684225905255,
> 0.630178116793598, 1.31534758842196, 1.33333958571746, 0.922032210748255,
> 0.429930193046174, 1.35881467717335, 0.790045927902363, 1.22484702570724,
> 0.808104508207897, 1.31185966817903, 1.51837686425553, 1.74105163638734,
> 1.80365598487402, 1.13240352674377, 1.50086243061644, 2.06355364280445,
> 0.439350890906039, 1.54692793444949, 1.78758216051046, 1.09043400023239,
> 0.811328376840514, 0.459192443530981, 0.695333473157298, 0.387995007681174,
> 0.784627063444921, 1.02282256375842, 0.382687104107726, 0.554290634950242,
> 0.130420456296453, 0.324194753224919, 0.31106140274139, 0.513473505828888,
> 0.878620320248701, 1.18404358659996, 0.136926837896477, 0, 0,
> 0.835588760032974, 0.558617235576616, 1.21002805866839, 0.769381068031404,
> 1.04514254228094, 0.373251847173678, 0.389005898972802, 0.183141006154896,
> 0.223596336820146, 0.315526423315647, 0.0930349732768131,
> 0.169959185212759,
> 0.161878841748425, 0, 0.0483041009105874, 0, 0, 0, 0.0777005553478052,
> 0, 0.153175826795441, 0.0428171049833677, 0, 0, 0, 0, 0, 0, 0,
> 0, 0, 0, 26.564295705327, 5.5893744508169, 7.22612934071834,
> 36.6563989567777, 0, 28.8967184437329, 28.4030370337251, 28.0886043901352,
> 26.1230935842208, 28.8895673910072, 42.6814210131968, 32.3555695551062,
> 0.76883326657205, 34.6159136622156, 38.329242204291, 56.4476583636484,
> 26.6249506083603, 31.3001451026823, 23.7339071829084, 23.3702284599355,
> 36.669903715038, 44.7377244306005, 31.2079335923023, 32.8613384312272,
> 29.4259634309146, 45.6112405959009, 48.1231689836687, 55.0037961570027,
> 32.9822316456421, 20.0382768189682, 26.0986380308655, 28.8915584506145,
> 28.7949023823068, 30.0278417498425, 58.8089779973569, 20.3602570111197,
> 29.6269605259023, 28.4404986724604, 30.2165182590977, 19.9204461889074,
> 31.1019196559556, 30.3847467747055, 36.8726911479995, 51.0618036275519,
> 23.5408013442579, 36.6948355347593, 27.4753860809429, 24.1341667099646,
> 27.5411488989643, 35.9021799354022, 19.7417897046158, 31.1403887303244,
> 46.1743622734049, 34.8235854891765, 22.1714704189293, 33.6805966894274,
> 35.2814908686112, 42.9767437212852, 38.1264997164547, 5.3651357974451,
> 42.8990434918385, 25.4908883698364, 25.99649502, 36.4958105490917,
> 40.8004126550705, 5.36867162116895, 0.00898476265269363, 0,
> 27.6810997945798,
> 28.7918300045713, 45.7577183830352, 35.9276318604787, 34.9717618087238,
> 29.620354272564, 24.6537513599869, 13.5363982464958, 25.8289073574818,
> 12.0090406245759, 4.753436805, 11.849214652228, 8.41410147611612,
> 0, 1.80855352862552, 1.1987530031681, 1.01148025243171, 0.495675369574172,
> 1.62701127228732, 0, 16.6288242287241, 1.23656061354912, 0.323708776035328,
> 0, 0.566916625204436, 0, 0, 0, 0, 0, 0, 0, 2.53578781871283,
> 3.50083667130797, 0, 0.98049572179098, 0, 3.57129673217304,
> 2.77298867949388,
> 2.12302645642669, 4.11923869203499, 4.69069462193674, 2.8698666062651,
> 2.05079837323067, 0.0602771574448942, 5.96454350250626, 2.26267114439802,
> 3.06911285674854, 2.04233129537404, 2.62181873844029, 1.51813653072598,
> 1.46193772981073, 2.69864635755833, 3.44016493913122, 2.50834832469627,
> 3.48170744166168, 1.00637581555435, 1.67065398473081, 4.18855363095027,
> 3.39649762611015, 1.72804613460423, 1.40053679329531, 2.37032387724109,
> 3.19332545080983, 2.49474373894248, 2.17800931288708, 2.7601484443213,
> 0.91266104095844, 1.93485048639199, 1.19692593420788, 1.79537330666258,
> 2.14020930767983, 3.0122526724942, 2.81112226980754, 3.54890724398174,
> 3.01022926452999, 2.38263226710738, 3.53569238341869, 3.47869329713911,
> 0.679333339820719, 2.4764260756438, 3.82615100065366, 2.20449890383871,
> 1.371303113329, 1.2427787019995, 1.73319133880954, 0.391268883238408,
> 1.73610193837913, 2.68494324646718, 1.77065393606844, 1.45079980147062,
> 0.763775702906329, 0.98566725668627, 0.37838763208699, 0.841811919286804,
> 1.46436462204795, 1.98409602726, 0.507005887891038, 0.465515668274195,
> 0, 1.873365675227, 1.69023864630648, 2.65530855919137, 2.34392199908302,
> 1.61917643594837, 1.05165934333345, 0.564642823436471, 0.121621029620328,
> 0.515007625737071, 0.524345809084086, 0.130898614090571, 0.332427740242623,
> 0.110214989555118, 0, 0.128642193589, 0.119407067173878, 0.128926224027295,
> 0.0622331866694357, 0.215645168287442, 0, 0.859343941945178,
> 0.0500810300696456, 0, 0, 0.0628746592609754), Organ =
> structure(as.integer(c(1,
> 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1,
> 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1,
> 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1,
> 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1,
> 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 3, 3, 3,
> 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3,
> 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3,
> 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3,
> 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3,
> 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2,
> 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2,
> 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2,
> 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2,
> 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2,
> 2, 2, 2, 2, 2)), .Label = c("Carc", "TD", "Foie"), class = c("ordered",
> "factor"))), .Names = c("Tps", "Conc", "Organ"), row.names = c("1",
> "2", "3", "4", "5", "6", "7", "8", "9", "10", "11", "12", "13",
> "14", "15", "16", "17", "18", "19", "20", "21", "22", "23", "24",
> "25", "26", "27", "28", "29", "30", "31", "32", "33", "34", "35",
> "36", "37", "38", "39", "40", "41", "42", "43", "44", "45", "46",
> "47", "48", "49", "50", "51", "52", "53", "54", "55", "56", "57",
> "58", "59", "60", "61", "62", "63", "64", "65", "66", "67", "68",
> "69", "70", "71", "72", "73", "74", "75", "76", "77", "78", "79",
> "80", "81", "82", "83", "84", "85", "86", "87", "88", "89", "90",
> "91", "92", "93", "94", "95", "96", "97", "98", "99", "100",
> "101", "102", "103", "104", "105", "106", "107", "108", "109",
> "110", "111", "112", "113", "114", "115", "116", "117", "118",
> "119", "120", "121", "122", "123", "124", "125", "126", "127",
> "128", "129", "130", "131", "132", "133", "134", "135", "136",
> "137", "138", "139", "140", "141", "142", "143", "144", "145",
> "146", "147", "148", "149", "150", "151", "152", "153", "154",
> "155", "156", "157", "158", "159", "160", "161", "162", "163",
> "164", "165", "166", "167", "168", "169", "170", "171", "172",
> "173", "174", "175", "176", "177", "178", "179", "180", "181",
> "182", "183", "184", "185", "186", "187", "188", "189", "190",
> "191", "192", "193", "194", "195", "196", "197", "198", "199",
> "200", "201", "202", "203", "204", "205", "206", "207", "208",
> "209", "210", "211", "212", "213", "214", "215", "216", "217",
> "218", "219", "220", "221", "222", "223", "224", "225", "226",
> "227", "228", "229", "230", "231", "232", "233", "234", "235",
> "236", "237", "238", "239", "240", "241", "242", "243", "244",
> "245", "246", "247", "248", "249", "250", "251", "252", "253",
> "254", "255", "256", "257", "258", "259", "260", "261", "262",
> "263", "264", "265", "266", "267", "268", "269", "270", "271",
> "272", "273", "274", "275", "276", "277", "278", "279", "280",
> "281", "282", "283", "284", "285", "286", "287", "288", "289",
> "290", "291", "292", "293", "294", "295", "296", "297", "298",
> "299", "300"), class = c("nfnGroupedData", "nfGroupedData", "groupedData",
> "data.frame"), formula = quote(Conc ~ Tps | Organ), FUN = function (x)
> max(x, na.rm = TRUE), order.groups = TRUE)
>
>
>
>
> Spencer Graves a écrit :
>> Regarding the following:
>>
>>> mymod3<-nlsList(Conc~Dose * exp(lKe+lKa-lCl) *
>>> (exp(-exp(lKe)*Tps)-exp(-exp(lKa)*Tps)) /(exp(lKa)-exp(lKe)),
>>> data=mydata,
>>> start= c(lKe=-2.77, lKa=-1.41, lCl=-1.13)
>>> Error in model.frame(formula, rownames, variables, varnames, extras,
>>> extranames, :
>>> variable lengths differ
>>
>> This example is NOT self contained and is entirely too
>> complicated for me to try to replicate it myself in a reasonable
>> period of time. I will therefore ask one short question: Are all the
>> variable names in the "nlsList" call either columns of "mydata" or
>> parameters to be estimated and therefore spelled out in "start"? If I
>> were you, I'd check this all very carefully, being especially careful
>> about the distinction between "lCl" and "lC1", in particular.
>>
>> If you'd like further help with this, I suggest you try to find
>> the simplest possible example that generates problem you don't
>> understand, then try to recast that example into one that is
>> completely self contained, either a data set in the standard R or nlme
>> distribution or numbers that one can generate with a very few lines
>> of code. If you use random numbers, please "set.seed", to increase
>> your confidence that someone else will see what you see. (And please
>> review the posting guide! "www.R-project.org/posting-guide.html".
>> Doing so may increase your chances of getting more useful information
>> more quickly.)
>>
>> spencer graves
>>
>> Patrick Giraudoux wrote:
>>
>>> Dear listers,
>>>
>>> I am trying to fit a model using nlsList() using alternately a
>>> SSfol() selfstart function or its developped equivalent formulae.
>>>
>>> This preliminary trial works well
>>>
>>> mydata<-groupedData(Conc~Tps|Organ,data=mydata)
>>> mymod1<-nls(Conc~SSfol(Dose,Tps,lKe,lKa,lCl),data=mydata)
>>>
>>> as well as a developped form:
>>>
>>> mymod2<-nls(Conc~Dose * exp(lKe+lKa-lCl) *
>>> (exp(-exp(lKe)*Tps)-exp(-exp(lKa)*Tps)) /(exp(lKa)-exp(lKe)),
>>> data=mydata,
>>> start= c(lKe=-2.77, lKa=-1.41, lCl=-1.13)
>>> )
>>>
>>> However when trying to fit the model with nlsList, I get:
>>>
>>> mymod3<-nlsList(Conc~Dose * exp(lKe+lKa-lCl) *
>>> (exp(-exp(lKe)*Tps)-exp(-exp(lKa)*Tps)) /(exp(lKa)-exp(lKe)),
>>> data=mydata,
>>> start= c(lKe=-2.77, lKa=-1.41, lCl=-1.13)
>>> )
>>> Error in model.frame(formula, rownames, variables, varnames, extras,
>>> extranames, :
>>> variable lengths differ
>>> Error in model.frame(formula, rownames, variables, varnames, extras,
>>> extranames, :
>>> variable lengths differ
>>> Error in model.frame(formula, rownames, variables, varnames, extras,
>>> extranames, :
>>> variable lengths differ
>>>
>>> Or specifying the grouping factor explicitely:
>>>
>>> mymod3<-nlsList(Conc~Dose * exp(lKe+lKa-lCl) *
>>> (exp(-exp(lKe)*Tps)-exp(-exp(lKa)*Tps)) /(exp(lKa)-exp(lKe))|Organ,
>>> data=mydata,
>>> start= c(lKe=-2.77, lKa=-1.41, lCl=-1.13)
>>> )
>>>
>>> Error in model.frame(formula, rownames, variables, varnames, extras,
>>> extranames, :
>>> variable lengths differ
>>> Error in model.frame(formula, rownames, variables, varnames, extras,
>>> extranames, :
>>> variable lengths differ
>>> Error in model.frame(formula, rownames, variables, varnames, extras,
>>> extranames, :
>>> variable lengths differ
>>>
>>>
>>> I cannot find out why the grouping factor cannot be used (it has the
>>> same length as the other variables...)
>>>
>>> Another strange thing occurs: in the example given in the help of
>>> nlsList.selfstart, the following command works well:
>>>
>>> fm1 <- nlsList(SSasympOff, CO2)
>>>
>>> However its seemingly equivalent applied to the case above fails:
>>>
>>> mymod4<-nlsList(SSfol,data=mydata)
>>> Error in eval(expr, envir, enclos) : object "input" not found
>>> Error in eval(expr, envir, enclos) : object "input" not found
>>> Error in eval(expr, envir, enclos) : object "input" not found
>>>
>>>
>>> Any hint/suggestion appreciated.
>>>
>>> Kind regards,
>>>
>>> Patrick Giraudoux
>>>
>>> ______________________________________________
>>> R-help at stat.math.ethz.ch mailing list
>>> https://stat.ethz.ch/mailman/listinfo/r-help
>>> PLEASE do read the posting guide!
>>> http://www.R-project.org/posting-guide.html
>>
>
> ______________________________________________
> R-help at stat.math.ethz.ch mailing list
> https://stat.ethz.ch/mailman/listinfo/r-help
> PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
>
--
Brian D. Ripley, ripley at stats.ox.ac.uk
Professor of Applied Statistics, http://www.stats.ox.ac.uk/~ripley/
University of Oxford, Tel: +44 1865 272861 (self)
1 South Parks Road, +44 1865 272866 (PA)
Oxford OX1 3TG, UK Fax: +44 1865 272595
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