From: Spencer Graves <spencer.graves_at_pdf.com>

Date: Sat 18 Feb 2006 - 04:23:24 EST

https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html Received on Sat Feb 18 04:48:11 2006

Date: Sat 18 Feb 2006 - 04:23:24 EST

Have you tried making mydata2$Dose the same length as everything else?

> Well, right, Dose was indeed in the global environment and not in the

*> data.frame. Changing it with
**>
**> mydata2$Dose<-100 # the real dose at the beginning of the experiment
**>
**> improves the thing in a sense... but I face a new error:
**>
**> mymod3<-nlsList(Conc+1 ~ 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 exp(-exp(lKa) * Conc + 1 ~ Tps) :
**> Non-numeric argument to mathematical function
**> Error in exp(-exp(lKa) * Conc + 1 ~ Tps) :
**> Non-numeric argument to mathematical function
**> Error in exp(-exp(lKa) * Conc + 1 ~ Tps) :
**> Non-numeric argument to mathematical function
**>
**> I have checked the variables in the data.frame with:
**>
**> > sapply(mydata2,is.factor)
**> Tps Conc Organ Dose
**> FALSE FALSE TRUE FALSE
**> > sapply(mydata2,is.character)
**> Tps Conc Organ Dose
**> FALSE FALSE FALSE FALSE
**>
**> So everything looks OK on this side...
**>
**> Furthermore, I have still this "old" error intact:
**>
**> > 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
**>
**>
**> I am really sorry for calling help and boring everybody on this likely
**> trivial issue (this looks like asking a community to participate to
**> debogging line by line, a shame!!!), but I must admit that I am really
**> lost...
**>
**> Thanks for your concern,
**>
**> Kind regards,
**>
**> Patrick
**>
**>
**> Prof Brian Ripley a écrit :
**>
*

>> 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@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@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@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 Received on Sat Feb 18 04:48:11 2006

*
This archive was generated by hypermail 2.1.8
: Fri 03 Mar 2006 - 03:42:34 EST
*